From 65771f08b00b41afc0609ece13ad56b78e67295b Mon Sep 17 00:00:00 2001 From: gmillot <gael.millot@pasteur.fr> Date: Mon, 3 Oct 2022 18:47:31 +0200 Subject: [PATCH] release v2.0: Compression added, tsv file optional --- README.md | 15 +- .../reports/dag.dot | 54 - .../reports/trace.txt | 4 - .../PL_family_WGS_slivar_1664357562/res.tsv | 111 -- .../PL_family_WGS_slivar_1664357562/res.vcf | 171 --- .../reports/dag.dot | 54 - .../reports/trace.txt | 4 - .../PL_family_WGS_slivar_1664358140/res.tsv | 1009 ----------------- .../PL_family_WGS_slivar_1664358140/res.vcf | 305 ----- .../reports/Log_info.txt | 0 .../reports/Run_info.txt | 6 +- .../reports/dag.dot | 70 ++ .../reports/report.html | 20 +- .../reports/slivar-functions.js | 0 .../reports/slivar_vcf_extraction.config | 11 +- .../reports/timeline.html | 14 +- .../reports/trace.txt | 6 + .../res.tsv.gz | Bin 0 -> 3581 bytes .../res.vcf.gz | Bin 0 -> 10184 bytes .../res.vcf.gz.tbi | Bin 0 -> 106 bytes .../reports/Log_info.txt | 0 .../reports/Run_info.txt | 6 +- .../reports/dag.dot | 70 ++ .../reports/report.html | 24 +- .../reports/slivar-functions.js | 0 .../reports/slivar_vcf_extraction.config | 5 +- .../reports/timeline.html | 14 +- .../reports/trace.txt | 6 + .../res.tsv.gz | Bin 0 -> 31589 bytes .../res.vcf.gz | Bin 0 -> 43971 bytes .../res.vcf.gz.tbi | Bin 0 -> 2709 bytes slivar_vcf_extraction.config | 15 +- slivar_vcf_extraction.nf | 71 +- 33 files changed, 283 insertions(+), 1782 deletions(-) delete mode 100644 example of results/PL_family_WGS_slivar_1664357562/reports/dag.dot delete mode 100644 example of results/PL_family_WGS_slivar_1664357562/reports/trace.txt delete mode 100644 example of results/PL_family_WGS_slivar_1664357562/res.tsv delete mode 100644 example of results/PL_family_WGS_slivar_1664357562/res.vcf delete mode 100644 example of results/PL_family_WGS_slivar_1664358140/reports/dag.dot delete mode 100644 example of results/PL_family_WGS_slivar_1664358140/reports/trace.txt delete mode 100644 example of results/PL_family_WGS_slivar_1664358140/res.tsv delete mode 100644 example of results/PL_family_WGS_slivar_1664358140/res.vcf rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/Log_info.txt (100%) rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/Run_info.txt (88%) create mode 100644 example of results/PL_family_WGS_slivar_1664807682/reports/dag.dot rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/report.html (99%) rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/slivar-functions.js (100%) rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/slivar_vcf_extraction.config (90%) rename example of results/{PL_family_WGS_slivar_1664357562 => PL_family_WGS_slivar_1664807682}/reports/timeline.html (99%) create mode 100644 example of results/PL_family_WGS_slivar_1664807682/reports/trace.txt create mode 100644 example of results/PL_family_WGS_slivar_1664807682/res.tsv.gz create mode 100644 example of results/PL_family_WGS_slivar_1664807682/res.vcf.gz create mode 100644 example of results/PL_family_WGS_slivar_1664807682/res.vcf.gz.tbi rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/Log_info.txt (100%) rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/Run_info.txt (86%) create mode 100644 example of results/PL_family_WGS_slivar_1664813804/reports/dag.dot rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/report.html (99%) rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/slivar-functions.js (100%) rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/slivar_vcf_extraction.config (97%) rename example of results/{PL_family_WGS_slivar_1664358140 => PL_family_WGS_slivar_1664813804}/reports/timeline.html (99%) create mode 100644 example of results/PL_family_WGS_slivar_1664813804/reports/trace.txt create mode 100644 example of results/PL_family_WGS_slivar_1664813804/res.tsv.gz create mode 100644 example of results/PL_family_WGS_slivar_1664813804/res.vcf.gz create mode 100644 example of results/PL_family_WGS_slivar_1664813804/res.vcf.gz.tbi diff --git a/README.md b/README.md index 2d60575..1ef449c 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ Use [slivar](https://github.com/brentp/slivar) on a VCF file to: <br /><ul><li>annotate <br /></li><li>filter (according to quality, family criteria, ect.) </li><br /><br /> -Return both a .vcf and a .tsv file +Return both an indexed .vcf.gz and a .tsv.gz file <br /><br /> Warning: the code uses these following commands of slivar (see protocol 143 for details): @@ -62,8 +62,8 @@ Thus, pay attention with the family_expr, sample and info parameters in the sliv <br /> | File | Description | | --- | --- | -| **PL_family_WGS_slivar_1664358140** | example of filtering and annotation, obtained using the whole dataset sample_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz" | -| **PL_family_WGS_slivar_1664357562** | example of annotation without slivar filtering, obtained using the example dataset sample_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf" | +| **PL_family_WGS_slivar_1664813804** | example of filtering and annotation, obtained using the whole dataset sample_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz" | +| **PL_family_WGS_slivar_1664807682** | example of annotation without slivar filtering, obtained using the example dataset sample_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf" | See the OUTPUT section for the description of the folder and files. @@ -200,9 +200,9 @@ rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot* **reports**: folder containing all the reports of the different processes including the *slivar_vcf_extraction.config* file used. <br /><br /> -**res.vcf**: annotated and filtered VCF file. +**res.vcf.gz**: annotated and filtered VCF file <br /><br /> -**res.tsv**: VCF file converted into a table, each row representing a different variant and a different patient, and with columns (depending on the tsv_info parameter): +**res.tsv.gz**: VCF file converted into a table, each row representing a different variant and a different patient, and with columns (depending on the tsv_info parameter): <br /> | File | Description | @@ -283,6 +283,11 @@ Gitlab developers ## WHAT'S NEW IN +### v2.0 + +Compression added, tsv file optional + + ### v1.0 Everything diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/dag.dot b/example of results/PL_family_WGS_slivar_1664357562/reports/dag.dot deleted file mode 100644 index 87727f1..0000000 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/dag.dot +++ /dev/null @@ -1,54 +0,0 @@ -digraph "dag" { -p1 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p1 -> p11 [label="vcf"]; - -p2 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p2 -> p11 [label="fun"]; - -p3 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p3 -> p11 [label="annot1"]; - -p4 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p4 -> p11 [label="annot2"]; - -p5 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p5 -> p11 [label="ped"]; - -p6 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p6 -> p11 [label="sample_expr"]; - -p7 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p7 -> p11 [label="pedigree_expr"]; - -p8 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p8 -> p11 [label="filter"]; - -p9 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p9 -> p11 [label="tsv_sample"]; - -p10 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p10 -> p11 [label="tsv_info"]; - -p12 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p12 -> p15 [label="config_file"]; - -p13 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p13 -> p15 [label="log_file"]; - -p14 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p14 -> p15 [label="fun"]; - -} diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/trace.txt b/example of results/PL_family_WGS_slivar_1664357562/reports/trace.txt deleted file mode 100644 index b6a8b0e..0000000 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/trace.txt +++ /dev/null @@ -1,4 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar -3 43/9f2a52 4517 Backup COMPLETED 0 2022-09-28 11:32:43.464 855ms 8ms 10.1% 0 0 104.1 KB 339 B -1 c2/724f64 4610 WorkflowVersion COMPLETED 0 2022-09-28 11:32:43.565 1.2s 469ms 17.7% 3.1 MB 19.2 MB 145.4 KB 1.6 KB -2 cf/fc450f 4553 slivar COMPLETED 0 2022-09-28 11:32:43.516 9.8s 9.2s 51.2% 1.9 GB 2 GB 438.3 MB 206.7 KB diff --git a/example of results/PL_family_WGS_slivar_1664357562/res.tsv b/example of results/PL_family_WGS_slivar_1664357562/res.tsv deleted file mode 100644 index f67efb8..0000000 --- a/example of results/PL_family_WGS_slivar_1664357562/res.tsv +++ /dev/null @@ -1,111 +0,0 @@ -#mode family_id sample_id chr:pos:ref:alt genotype(sample,dad,mom) AC AF AN BaseQRankSum DB DP ExcessHet FS InbreedingCoeff MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR VQSLOD culprit CSQ cadd_phred gno_non_neuro_af_all gno_non_neuro_af_nfe gno_non_neuro_nhomalt_all gno_non_neuro_nhomalt_nfe highest_impact_order all depths(sample,dad,mom) allele_balance(sample,dad,mom) -all fam_pl C0011JY chr1:10146:AC:A 0,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 143,.,. 0,.,. -all fam_pl C0011JZ chr1:10146:AC:A 1,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.809524,.,. -all fam_pl C0011K1 chr1:10146:AC:A 2,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 13,.,. 0.846154,.,. -all fam_pl C0011K2 chr1:10146:AC:A 0,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 126,.,. 0,.,. -all fam_pl C0011K3 chr1:10146:AC:A 1,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.681818,.,. -all fam_pl C0011K5 chr1:10146:AC:A 1,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 12,.,. 0.666667,.,. -all fam_pl C0011KA chr1:10146:AC:A 0,.,0 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 105,.,126 0,.,0 -all fam_pl C0011KB chr1:10146:AC:A 0,.,0 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 147,.,126 0,.,0 -all fam_pl IP00FNP chr1:10146:AC:A 2,.,1 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 98,.,21 0.938776,.,0.809524 -all fam_pl IP00FNW chr1:10146:AC:A 0,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 121,.,. 0,.,. -all fam_pl IP00FNY chr1:10146:AC:A 0,.,. 7 0.318 22 0.341 DB 1004 0.5742 32.034 0.2598 7 0.318 35.31 -0.403 10.39 1.02 3.687 1.66 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034||||| -1 0.521818 0.481386 276 141 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 147,.,. 0,.,. -all fam_pl C0011JY chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 87,.,. 0,.,. -all fam_pl C0011JZ chr1:10177:A:C -1,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 69,.,. 0,.,. -all fam_pl C0011K1 chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 91,.,. 0,.,. -all fam_pl C0011K2 chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 77,.,. 0,.,. -all fam_pl C0011K3 chr1:10177:A:C 1,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 15,.,. 0.8,.,. -all fam_pl C0011K5 chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 69,.,. 0,.,. -all fam_pl C0011KA chr1:10177:A:C -1,.,0 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 80,.,77 0,.,0 -all fam_pl C0011KB chr1:10177:A:C 0,.,0 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 90,.,77 0,.,0 -all fam_pl IP00FNP chr1:10177:A:C 0,.,-1 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 66,.,69 0,.,0 -all fam_pl IP00FNW chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 81,.,. 0,.,. -all fam_pl IP00FNY chr1:10177:A:C 0,.,. 1 0.056 18 1.72 DB 823 3.0103 4.301 -0.1873 3 0.167 32.12 1.68 13.29 1.01 2.833 -11.15 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034||||| -1 0.155172 0.134146 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 92,.,. 0,.,. -all fam_pl C0011JY chr1:10255:A:AAACCCTAACCCT -1,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 137,.,. 0,.,. -all fam_pl C0011JZ chr1:10255:A:AAACCCTAACCCT -1,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 113,.,. 0,.,. -all fam_pl C0011K1 chr1:10255:A:AAACCCTAACCCT 0,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 3,.,. 0,.,. -all fam_pl C0011K2 chr1:10255:A:AAACCCTAACCCT -1,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 92,.,. 0,.,. -all fam_pl C0011K3 chr1:10255:A:AAACCCTAACCCT -1,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 117,.,. 0,.,. -all fam_pl C0011K5 chr1:10255:A:AAACCCTAACCCT -1,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 103,.,. 0,.,. -all fam_pl C0011KA chr1:10255:A:AAACCCTAACCCT -1,.,-1 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 102,.,92 0,.,0 -all fam_pl C0011KB chr1:10255:A:AAACCCTAACCCT 2,.,-1 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 1,.,92 1,.,0 -all fam_pl IP00FNP chr1:10255:A:AAACCCTAACCCT 0,.,-1 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 111,.,113 0,.,0 -all fam_pl IP00FNW chr1:10255:A:AAACCCTAACCCT 0,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 77,.,. 0,.,. -all fam_pl IP00FNY chr1:10255:A:AAACCCTAACCCT 0,.,. 2 0.2 10 . 974 0.2482 0 0.2499 3 0.3 27.07 . 25.36 . 1.609 -0.6117 MQ AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 103,.,. 0,.,. -all fam_pl C0011JY chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 137,.,. 0,.,. -all fam_pl C0011JZ chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 123,.,. 0,.,. -all fam_pl C0011K1 chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 128,.,. 0,.,. -all fam_pl C0011K2 chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 126,.,. 0,.,. -all fam_pl C0011K3 chr1:10335:AACCCTAACCCTAACCCT:A 1,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 9,.,. 0.222222,.,. -all fam_pl C0011K5 chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 120,.,. 0,.,. -all fam_pl C0011KA chr1:10335:AACCCTAACCCTAACCCT:A -1,.,0 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 2,.,126 0,.,0 -all fam_pl C0011KB chr1:10335:AACCCTAACCCTAACCCT:A -1,.,0 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 0,.,126 0,.,0 -all fam_pl IP00FNP chr1:10335:AACCCTAACCCTAACCCT:A 0,.,0 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 5,.,123 0,.,0 -all fam_pl IP00FNW chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 120,.,. 0,.,. -all fam_pl IP00FNY chr1:10335:AACCCTAACCCTAACCCT:A 0,.,. 1 0.056 18 0.282 941 3.0103 6.532 -0.0826 2 0.111 36.92 -1.732 4.41 -0.035 0.016 -1.04 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 153,.,. 0,.,. -all fam_pl C0011JY chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 159,.,. 0,.,. -all fam_pl C0011JZ chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 140,.,. 0,.,. -all fam_pl C0011K1 chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 149,.,. 0,.,. -all fam_pl C0011K2 chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 129,.,. 0,.,. -all fam_pl C0011K3 chr1:10337:CCCTAA:C 1,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.857143,.,. -all fam_pl C0011K5 chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 138,.,. 0,.,. -all fam_pl C0011KA chr1:10337:CCCTAA:C -1,.,0 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 2,.,129 0,.,0 -all fam_pl C0011KB chr1:10337:CCCTAA:C -1,.,0 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 0,.,129 0,.,0 -all fam_pl IP00FNP chr1:10337:CCCTAA:C 0,.,0 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 6,.,140 0,.,0 -all fam_pl IP00FNW chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 135,.,. 0,.,. -all fam_pl IP00FNY chr1:10337:CCCTAA:C 0,.,. 1 0.056 18 -0.14 1040 3.0103 0 0.3447 1 0.056 37.66 0.967 22.29 -1.593 1.609 -1.779 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034||||| -1 0 0 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 157,.,. 0,.,. -all fam_pl C0011JY chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 128,.,. 0,.,. -all fam_pl C0011JZ chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 112,.,. 0,.,. -all fam_pl C0011K1 chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 122,.,. 0,.,. -all fam_pl C0011K2 chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 116,.,. 0,.,. -all fam_pl C0011K3 chr1:10354:C:A 1,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.454545,.,. -all fam_pl C0011K5 chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 101,.,. 0,.,. -all fam_pl C0011KA chr1:10354:C:A 0,.,0 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 2,.,116 0,.,0 -all fam_pl C0011KB chr1:10354:C:A 0,.,0 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 5,.,116 0,.,0 -all fam_pl IP00FNP chr1:10354:C:A 0,.,0 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 10,.,112 0,.,0 -all fam_pl IP00FNW chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 172,.,. 0,.,. -all fam_pl IP00FNY chr1:10354:C:A 0,.,. 1 0.045 22 -0.114 986 3.0103 10.296 -0.2374 2 0.091 32.62 3.07 14.64 1.29 3.604 -16.72 MQ A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034||||| -1 0.0625 0.0695187 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 183,.,. 0,.,. -all fam_pl C0011JY chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 133,.,. 0,.,. -all fam_pl C0011JZ chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 97,.,. 0,.,. -all fam_pl C0011K1 chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 124,.,. 0,.,. -all fam_pl C0011K2 chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 105,.,. 0,.,. -all fam_pl C0011K3 chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 20,.,. 0,.,. -all fam_pl C0011K5 chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 96,.,. 0,.,. -all fam_pl C0011KA chr1:10387:T:C 0,.,0 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 10,.,105 0,.,0 -all fam_pl C0011KB chr1:10387:T:C 0,.,0 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 8,.,105 0,.,0 -all fam_pl IP00FNP chr1:10387:T:C 1,.,0 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 27,.,97 0.259259,.,0 -all fam_pl IP00FNW chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 186,.,. 0,.,. -all fam_pl IP00FNY chr1:10387:T:C 0,.,. 1 0.045 22 1.17 1037 3.0103 1.983 -0.2945 2 0.091 32.44 0.028 3.54 -1.246 1.609 -7.425 MQ C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034||||| -1 -1 -1 -1 -1 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 209,.,. 0,.,. -all fam_pl C0011JY chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 133,.,. 0,.,. -all fam_pl C0011JZ chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 107,.,. 0,.,. -all fam_pl C0011K1 chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 126,.,. 0,.,. -all fam_pl C0011K2 chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 105,.,. 0,.,. -all fam_pl C0011K3 chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 26,.,. 0,.,. -all fam_pl C0011K5 chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 93,.,. 0,.,. -all fam_pl C0011KA chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,0 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 11,.,105 0,.,0 -all fam_pl C0011KB chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,0 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 7,.,105 0,.,0 -all fam_pl IP00FNP chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,0 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 28,.,107 0,.,0 -all fam_pl IP00FNW chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 1,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.55,.,. -all fam_pl IP00FNY chr1:10390:CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:C 0,.,. 1 0.045 22 2.09 928 3.0103 3.285 -0.2574 2 0.091 37.08 1.87 15.94 -2.856 1.532 -3.165 ReadPosRankSum -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034||||| -1 0.0653409 0.0840336 0 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 200,.,. 0,.,. -all fam_pl C0011JY chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 121,.,. 0,.,. -all fam_pl C0011JZ chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 85,.,. 0,.,. -all fam_pl C0011K1 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 121,.,. 0,.,. -all fam_pl C0011K2 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 99,.,. 0,.,. -all fam_pl C0011K3 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 22,.,. 0,.,. -all fam_pl C0011K5 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 95,.,. 0,.,. -all fam_pl C0011KA chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 18,.,99 0,.,0 -all fam_pl C0011KB chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 15,.,99 0,.,0 -all fam_pl IP00FNP chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 28,.,85 0,.,0 -all fam_pl IP00FNW chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 1,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.55,.,. -all fam_pl IP00FNY chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:* 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -1 -1 -1 -1 -1 2147483646 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 185,.,. 0,.,. -all fam_pl C0011JY chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 121,.,. 0,.,. -all fam_pl C0011JZ chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 85,.,. 0,.,. -all fam_pl C0011K1 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 121,.,. 0,.,. -all fam_pl C0011K2 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 99,.,. 0,.,. -all fam_pl C0011K3 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 1,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.12,.,. -all fam_pl C0011K5 chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 95,.,. 0,.,. -all fam_pl C0011KA chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 18,.,99 0,.,0 -all fam_pl C0011KB chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 15,.,99 0,.,0 -all fam_pl IP00FNP chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,0 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 28,.,85 0,.,0 -all fam_pl IP00FNW chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 9,.,. 0,.,. -all fam_pl IP00FNY chr1:10403:ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC:A 0,.,. 1 0.045 22 0.961 861 3.2222 5.418 -0.1288 1 0.045 41.48 -1.054 1.51 -0.352 1.739 -1.977 MQ -|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034||||| -1 0.239586 0.259883 2 0 51 C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY 185,.,. 0,.,. diff --git a/example of results/PL_family_WGS_slivar_1664357562/res.vcf b/example of results/PL_family_WGS_slivar_1664357562/res.vcf deleted file mode 100644 index 6363319..0000000 --- a/example of results/PL_family_WGS_slivar_1664357562/res.vcf +++ /dev/null @@ -1,171 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER=<ID=PASS,Description="All filters passed"> -##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> -##FILTER=<ID=LowQual,Description="Low quality"> -##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.5351 <= x < -0.4741"> -##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -20794.8907"> -##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -20794.8907 <= x < -4.5351"> -##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39178.8364"> -##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39178.8364 <= x < -2.9039"> -##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> -##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> -##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> -##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> -##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-0-gcfedb67,Date="Tue Aug 04 18:41:02 CEST 2020",Epoch=1596559262546,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/dev/shm/hs37d5_all_chr.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.g.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-vqsr.vcf.gz --truth-sensitivity-filter-level 99.0 --mode INDEL --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:50:15 PM CEST"> -##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --truth-sensitivity-filter-level 99.5 --mode SNP --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-no-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:31:29 PM CEST"> -##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path /local/scratch/tmp/38734053_1//Dyslexia.chr1.1-1000000 --overwrite-existing-genomicsdb-workspace true --batch-size 50 --consolidate true --sample-name-map /local/scratch/tmp/38734053_1/sample.map --reader-threads 1 --intervals chr1:1-1000000 --interval-padding 500 --tmp-dir /local/scratch/tmp/38734053_1//tmp/ --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --validate-sample-name-map false --merge-input-intervals false --max-num-intervals-to-import-in-parallel 1 --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 15, 2021 3:11:49 PM CEST"> -##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /local/scratch/tmp/38743216_1/Dyslexia.chr1.1-1000000.genotyped.vcf.gz --only-output-calls-starting-in-intervals true --dbsnp /pasteur/zeus/projets/p02/ghfc_wgs_zeus/tools/ngs-workflow/references/GRCh37/chr/gatk-bundle/dbsnp_138.hg19.vcf.gz --variant gendb:///local/scratch/tmp/38743216_1//Dyslexia.chr1.1-1000000 --intervals chr1:1-1000000 --reference references/GRCh37/chr/hs37d5.fa --annotation-group StandardAnnotation --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.8.1",Date="September 15, 2021 3:30:43 PM CEST"> -##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --standard-min-confidence-threshold-for-calling 10.0 --output /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf --intervals /ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01_overlap.bed --input /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/MAPPING_C0011JY/reliable.realign.recal/A592_DA_C0011JY_H72NKCCX2_hs37d5_MERGE_PE_1_01.reliable.realign.recal.bam --reference /dev/shm/hs37d5_all_chr.fasta --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.1.0.0,Date="August 4, 2020 4:14:40 PM CEST"> -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> -##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> -##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> -##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model"> -##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"> -##bcftools_normCommand=norm -m - -w 10000 -f references/GRCh37/chr/hs37d5.fa; Date=Wed Sep 15 15:31:06 2021 -##bcftools_normVersion=1.12+htslib-1.12 -##contig=<ID=chr1,length=249250621> -##contig=<ID=chr2,length=243199373> -##contig=<ID=chr3,length=198022430> -##contig=<ID=chr4,length=191154276> -##contig=<ID=chr5,length=180915260> -##contig=<ID=chr6,length=171115067> -##contig=<ID=chr7,length=159138663> -##contig=<ID=chr8,length=146364022> -##contig=<ID=chr9,length=141213431> -##contig=<ID=chr10,length=135534747> -##contig=<ID=chr11,length=135006516> -##contig=<ID=chr12,length=133851895> -##contig=<ID=chr13,length=115169878> -##contig=<ID=chr14,length=107349540> -##contig=<ID=chr15,length=102531392> -##contig=<ID=chr16,length=90354753> -##contig=<ID=chr17,length=81195210> -##contig=<ID=chr18,length=78077248> -##contig=<ID=chr19,length=59128983> -##contig=<ID=chr20,length=63025520> -##contig=<ID=chr21,length=48129895> -##contig=<ID=chr22,length=51304566> -##contig=<ID=chrX,length=155270560> -##contig=<ID=chrY,length=59373566> -##contig=<ID=chrMT,length=16569> -##contig=<ID=GL000207.1,length=4262> -##contig=<ID=GL000226.1,length=15008> -##contig=<ID=GL000229.1,length=19913> -##contig=<ID=GL000231.1,length=27386> -##contig=<ID=GL000210.1,length=27682> -##contig=<ID=GL000239.1,length=33824> -##contig=<ID=GL000235.1,length=34474> -##contig=<ID=GL000201.1,length=36148> -##contig=<ID=GL000247.1,length=36422> -##contig=<ID=GL000245.1,length=36651> -##contig=<ID=GL000197.1,length=37175> -##contig=<ID=GL000203.1,length=37498> -##contig=<ID=GL000246.1,length=38154> -##contig=<ID=GL000249.1,length=38502> -##contig=<ID=GL000196.1,length=38914> -##contig=<ID=GL000248.1,length=39786> -##contig=<ID=GL000244.1,length=39929> -##contig=<ID=GL000238.1,length=39939> -##contig=<ID=GL000202.1,length=40103> -##contig=<ID=GL000234.1,length=40531> -##contig=<ID=GL000232.1,length=40652> -##contig=<ID=GL000206.1,length=41001> -##contig=<ID=GL000240.1,length=41933> -##contig=<ID=GL000236.1,length=41934> -##contig=<ID=GL000241.1,length=42152> -##contig=<ID=GL000243.1,length=43341> -##contig=<ID=GL000242.1,length=43523> -##contig=<ID=GL000230.1,length=43691> -##contig=<ID=GL000237.1,length=45867> -##contig=<ID=GL000233.1,length=45941> -##contig=<ID=GL000204.1,length=81310> -##contig=<ID=GL000198.1,length=90085> -##contig=<ID=GL000208.1,length=92689> -##contig=<ID=GL000191.1,length=106433> -##contig=<ID=GL000227.1,length=128374> -##contig=<ID=GL000228.1,length=129120> -##contig=<ID=GL000214.1,length=137718> -##contig=<ID=GL000221.1,length=155397> -##contig=<ID=GL000209.1,length=159169> -##contig=<ID=GL000218.1,length=161147> -##contig=<ID=GL000220.1,length=161802> -##contig=<ID=GL000213.1,length=164239> -##contig=<ID=GL000211.1,length=166566> -##contig=<ID=GL000199.1,length=169874> -##contig=<ID=GL000217.1,length=172149> -##contig=<ID=GL000216.1,length=172294> -##contig=<ID=GL000215.1,length=172545> -##contig=<ID=GL000205.1,length=174588> -##contig=<ID=GL000219.1,length=179198> -##contig=<ID=GL000224.1,length=179693> -##contig=<ID=GL000223.1,length=180455> -##contig=<ID=GL000195.1,length=182896> -##contig=<ID=GL000212.1,length=186858> -##contig=<ID=GL000222.1,length=186861> -##contig=<ID=GL000200.1,length=187035> -##contig=<ID=GL000193.1,length=189789> -##contig=<ID=GL000194.1,length=191469> -##contig=<ID=GL000225.1,length=211173> -##contig=<ID=GL000192.1,length=547496> -##contig=<ID=NC_007605,length=171823> -##contig=<ID=hs37d5,length=35477943> -##reference=file:///dev/shm/hs37d5_all_chr.fasta -##source=ApplyVQSR -##source=GenomicsDBImport -##source=GenotypeGVCFs -##source=HaplotypeCaller -##source=SelectVariants -##bcftools_normCommand=norm -m - -w 1000 -c s -f references/GRCh37/chr/hs37d5.fa --threads 3 -Oz -o /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/splitted/Dyslexia.gatk-vqsr.splitted.chr1.1-10000000.norm.vcf.gz; Date=Thu Sep 16 12:54:23 2021 -##VEP="v104" time="2021-09-16 12:54:40" cache="tools/ensembl-vep-104.3/data/homo_sapiens/104_GRCh37" ensembl-variation=104.20f5335 ensembl-funcgen=104.f1c7762 ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2" -##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET"> -##INFO=<ID=cadd_phred,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=cadd_phred_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_af_all,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_af_all_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_af_nfe,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_af_nfe_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_all,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_all_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_nfe,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_nfe_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=all,Number=.,Type=String,Description="added by slivar with expression: 'sample.DP >= 0' from Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf"> -##INFO=<ID=impactful,Number=0,Type=Flag,Description="variant is impactful according to slivar and impacts added by VEP/snpEff/bcftools (https://github.com/brentp/slivar/wiki/impactful)"> -##INFO=<ID=genic,Number=0,Type=Flag,Description="variant is genic according to slivar and impacts added by VEP/snpEff/bcftools (https://github.com/brentp/slivar/wiki/impactful)"> -##INFO=<ID=highest_impact_order,Number=1,Type=Integer,Description="impact order (lower is higher) of this variant across all genes and transcripts it overlaps. this integer can be used as a look into the order list to get the actual impact"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT C0011JY C0011JZ C0011K1 C0011K2 C0011K3 C0011K5 C0011KA C0011KB IP00FNP IP00FNW IP00FNY -chr1 10146 rs375931351 AC A 1724.92 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.341;DB;DP=1004;ExcessHet=0.5742;FS=32.034;InbreedingCoeff=0.2598;MLEAC=7;MLEAF=0.318;MQ=35.31;MQRankSum=-0.403;QD=10.39;ReadPosRankSum=1.02;SOR=3.687;VQSLOD=1.66;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1863|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1722|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4257|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1725|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1727|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4264|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4216|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0.521818;gno_non_neuro_af_nfe=0.481386;gno_non_neuro_nhomalt_all=276;gno_non_neuro_nhomalt_nfe=141;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:143,0:143:99:.:.:0,120,1800:. 0/1:4,17:21:64:.:.:294,0,64:. 1/1:2,11:13:12:.:.:232,12,0:. 0/0:126,0:126:72:.:.:0,72,2864:. 0|1:7,15:22:99:0|1:10146_AC_A:318,0,158:10146 0/1:4,8:12:48:.:.:92,0,48:. 0/0:105,0:105:0:.:.:0,0,1112:. 0/0:147,0:147:9:.:.:0,9,2908:. 1/1:6,92:98:56:.:.:814,56,0:. 0/0:121,0:121:99:.:.:0,120,1800:. 0/0:147,0:147:99:.:.:0,120,1800:. -chr1 10177 rs201752861 A C 199.3 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.056;AN=18;BaseQRankSum=1.72;DB;DP=823;ExcessHet=3.0103;FS=4.301;InbreedingCoeff=-0.1873;MLEAC=3;MLEAF=0.167;MQ=32.12;MQRankSum=1.68;QD=13.29;ReadPosRankSum=1.01;SOR=2.833;VQSLOD=-11.15;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1833|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1692|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4227|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1695|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1697|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4234|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4186|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0.155172;gno_non_neuro_af_nfe=0.134146;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_nfe=0;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:87,0:87:0:.:.:0,0,433:. ./.:69,0:69:.:.:.:0,0,0:. 0/0:91,0:91:0:.:.:0,0,256:. 0/0:77,0:77:0:.:.:0,0,37:. 0|1:3,12:15:99:0|1:10146_AC_A:200,0,103:10146 0/0:69,0:69:0:.:.:0,0,295:. ./.:80,0:80:.:.:.:0,0,0:. 0/0:90,0:90:0:.:.:0,0,102:. 0/0:66,0:66:0:.:.:0,0,731:. 0/0:81,0:81:0:.:.:0,0,1688:. 0/0:92,0:92:0:.:.:0,0,1127:. -chr1 10255 . A AAACCCTAACCCT 41.43 VQSRTrancheINDEL99.00to99.90 AC=2;AF=0.2;AN=10;DP=974;ExcessHet=0.2482;FS=0;InbreedingCoeff=0.2499;MLEAC=3;MLEAF=0.3;MQ=27.07;QD=25.36;SOR=1.609;VQSLOD=-0.6117;culprit=MQ;CSQ=AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|YES||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1754|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1613|1||HGNC|37102|YES||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4148|-1||HGNC|38034|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1616|1||HGNC|37102|||||,AACCCTAACCCT|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1618|1||HGNC|37102|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4155|-1||HGNC|38034|||||,AACCCTAACCCT|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4107|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL ./.:137,0:137:.:0,0,0 ./.:113,0:113:.:0,0,0 0/0:3,0:3:6:0,6,90 ./.:92,0:92:.:0,0,0 ./.:117,0:117:.:0,0,0 ./.:103,0:103:.:0,0,0 ./.:102,0:102:.:0,0,0 1/1:0,1:1:3:45,3,0 0/0:111,0:111:0:0,0,817 0/0:77,0:77:0:0,0,326 0/0:103,0:103:0:0,0,951 -chr1 10335 . AACCCTAACCCTAACCCT A 39.68 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.056;AN=18;BaseQRankSum=0.282;DP=941;ExcessHet=3.0103;FS=6.532;InbreedingCoeff=-0.0826;MLEAC=2;MLEAF=0.111;MQ=36.92;MQRankSum=-1.732;NEGATIVE_TRAIN_SITE;QD=4.41;ReadPosRankSum=-0.035;SOR=0.016;VQSLOD=-1.04;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1658|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1517|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4052|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1522|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4059|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4011|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:137,0:137:0:0,0,724 0/0:123,0:123:0:0,0,1204 0/0:128,0:128:0:0,0,162 0/0:126,0:126:0:0,0,1099 0/1:7,2:9:44:44,0,252 0/0:120,0:120:0:0,0,490 ./.:2,0:2:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:5,0:5:9:0,9,135 0/0:120,0:120:0:0,0,1141 0/0:153,0:153:99:0,120,1800 -chr1 10337 . CCCTAA C 156.01 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.056;AN=18;BaseQRankSum=-0.14;DP=1040;ExcessHet=3.0103;FS=0;InbreedingCoeff=0.3447;MLEAC=1;MLEAF=0.056;MQ=37.66;MQRankSum=0.967;NEGATIVE_TRAIN_SITE;QD=22.29;ReadPosRankSum=-1.593;SOR=1.609;VQSLOD=-1.779;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1668|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1527|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4062|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1530|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1532|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4069|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4021|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0;gno_non_neuro_af_nfe=0;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_nfe=0;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:159,0:159:99:0,120,1800 0/0:140,0:140:98:0,98,3458 0/0:149,0:149:87:0,87,3684 0/0:129,0:129:99:0,116,1800 0/1:1,6:9:86:212,0,86 0/0:138,0:138:99:0,120,1800 ./.:2,0:2:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:6,0:6:12:0,12,180 0/0:135,0:135:99:0,120,1800 0/0:157,0:157:99:0,120,1800 -chr1 10354 . C A 161.08 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.045;AN=22;BaseQRankSum=-0.114;DP=986;ExcessHet=3.0103;FS=10.296;InbreedingCoeff=-0.2374;MLEAC=2;MLEAF=0.091;MQ=32.62;MQRankSum=3.07;QD=14.64;ReadPosRankSum=1.29;SOR=3.604;VQSLOD=-16.72;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|YES||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1656|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1515|1||HGNC|37102|YES||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4050|-1||HGNC|38034|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1518|1||HGNC|37102|||||,A|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1520|1||HGNC|37102|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4057|-1||HGNC|38034|||||,A|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4009|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0.0625;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0695187;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:128,0:128:0:.:.:0,0,398:. 0/0:112,0:112:0:.:.:0,0,867:. 0/0:122,0:122:0:.:.:0,0,155:. 0/0:116,0:116:0:.:.:0,0,1020:. 0/1:6,5:11:99:.:.:168,0,162:. 0/0:101,0:101:0:.:.:0,0,655:. 0/0:2,0:2:6:.:.:0,6,59:. 0|0:5,0:5:18:0|1:10297_C_T:0,18,260:10297 0/0:10,0:10:24:.:.:0,24,360:. 0/0:172,0:172:44:.:.:0,44,4150:. 0/0:183,0:183:0:.:.:0,0,946:. -chr1 10387 . T C 95.49 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.045;AN=22;BaseQRankSum=1.17;DP=1037;ExcessHet=3.0103;FS=1.983;InbreedingCoeff=-0.2945;MLEAC=2;MLEAF=0.091;MQ=32.44;MQRankSum=0.028;QD=3.54;ReadPosRankSum=-1.246;SOR=1.609;VQSLOD=-7.425;culprit=MQ;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|YES||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1623|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1482|1||HGNC|37102|YES||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4017|-1||HGNC|38034|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1485|1||HGNC|37102|||||,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1487|1||HGNC|37102|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4024|-1||HGNC|38034|||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3976|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:133,0:133:0:0,0,2958 0/0:97,0:97:0:0,0,1738 0/0:124,0:124:0:0,0,2139 0/0:105,0:105:0:0,0,1714 0/0:20,0:20:0:0,0,516 0/0:96,0:96:0:0,0,1327 0/0:10,0:10:30:0,30,277 0/0:8,0:8:24:0,24,218 0/1:20,7:27:99:100,0,472 0/0:186,0:186:0:0,0,2777 0/0:209,0:209:0:0,0,2587 -chr1 10390 . CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA C 318.84 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.045;AN=22;BaseQRankSum=2.09;DP=928;ExcessHet=3.0103;FS=3.285;InbreedingCoeff=-0.2574;MLEAC=2;MLEAF=0.091;MQ=37.08;MQRankSum=1.87;NEGATIVE_TRAIN_SITE;QD=15.94;ReadPosRankSum=-2.856;SOR=1.532;VQSLOD=-3.165;culprit=ReadPosRankSum;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1577|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1436|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1439|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1441|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3978|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3930|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0.0653409;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0840336;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:133,0:133:0:.:.:0,0,2953:. 0/0:107,0:107:0:.:.:0,0,2104:. 0/0:126,0:126:0:.:.:0,0,1984:. 0/0:105,0:105:0:.:.:0,0,1714:. 0/0:26,0:26:82:.:.:0,82,1200:. 0/0:93,0:93:0:.:.:0,0,1565:. 0/0:11,0:11:0:.:.:0,0,283:. 0|0:7,0:7:25:0|1:10297_C_T:0,25,351:10297 0/0:28,0:28:81:.:.:0,81,1215:. 0/1:9,11:20:99:.:.:325,0,309:. 0/0:200,0:200:0:.:.:0,0,4329:. -chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC * 67.82 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.045;AN=22;BaseQRankSum=0.961;DP=861;ExcessHet=3.2222;FS=5.418;InbreedingCoeff=-0.1288;MLEAC=1;MLEAF=0.045;MQ=41.48;MQRankSum=-1.054;NEGATIVE_TRAIN_SITE;QD=1.51;ReadPosRankSum=-0.352;SOR=1.739;VQSLOD=-1.977;culprit=MQ;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=2147483646;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:121,0:121:99:0,120,1800 0/0:85,0:85:0:0,0,1394 0/0:121,0:121:20:0,20,3067 0/0:99,0:99:99:0,117,1800 0/0:22,0:25:79:79,124,1098 0/0:95,0:95:85:0,85,2510 0/0:18,0:18:48:0,48,720 0/0:15,0:15:39:0,39,585 0/0:28,0:28:48:0,48,720 0/1:9,11:20:99:325,0,309 0/0:185,0:185:99:0,120,1800 -chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A 67.82 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.045;AN=22;BaseQRankSum=0.961;DP=861;ExcessHet=3.2222;FS=5.418;InbreedingCoeff=-0.1288;MLEAC=1;MLEAF=0.045;MQ=41.48;MQRankSum=-1.054;NEGATIVE_TRAIN_SITE;QD=1.51;ReadPosRankSum=-0.352;SOR=1.739;VQSLOD=-1.977;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|YES||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1570|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1429|1||HGNC|37102|YES||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3964|-1||HGNC|38034|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1432|1||HGNC|37102|||||,-|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1434|1||HGNC|37102|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||3971|-1||HGNC|38034|||||,-|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||3923|-1||HGNC|38034|||||;cadd_phred=-1;gno_non_neuro_af_all=0.239586;gno_non_neuro_af_nfe=0.259883;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_nfe=0;highest_impact_order=51;all=C0011JY,C0011JZ,C0011K1,C0011K2,C0011K3,C0011K5,C0011KA,C0011KB,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:121,0:121:99:0,120,1800 0/0:85,0:85:0:0,0,1394 0/0:121,0:121:20:0,20,3067 0/0:99,0:99:99:0,117,1800 0/1:22,3:25:79:79,0,1057 0/0:95,0:95:85:0,85,2510 0/0:18,0:18:48:0,48,720 0/0:15,0:15:39:0,39,585 0/0:28,0:28:48:0,48,720 0/0:9,0:20:99:325,352,693 0/0:185,0:185:99:0,120,1800 diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/dag.dot b/example of results/PL_family_WGS_slivar_1664358140/reports/dag.dot deleted file mode 100644 index 87727f1..0000000 --- a/example of results/PL_family_WGS_slivar_1664358140/reports/dag.dot +++ /dev/null @@ -1,54 +0,0 @@ -digraph "dag" { -p1 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p1 -> p11 [label="vcf"]; - -p2 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p2 -> p11 [label="fun"]; - -p3 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p3 -> p11 [label="annot1"]; - -p4 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p4 -> p11 [label="annot2"]; - -p5 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p5 -> p11 [label="ped"]; - -p6 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p6 -> p11 [label="sample_expr"]; - -p7 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p7 -> p11 [label="pedigree_expr"]; - -p8 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p8 -> p11 [label="filter"]; - -p9 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p9 -> p11 [label="tsv_sample"]; - -p10 [shape=point,label="",fixedsize=true,width=0.1]; -p11 [label="slivar"]; -p10 -> p11 [label="tsv_info"]; - -p12 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p12 -> p15 [label="config_file"]; - -p13 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p13 -> p15 [label="log_file"]; - -p14 [shape=point,label="",fixedsize=true,width=0.1]; -p15 [label="Backup"]; -p14 -> p15 [label="fun"]; - -} diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/trace.txt b/example of results/PL_family_WGS_slivar_1664358140/reports/trace.txt deleted file mode 100644 index 18d9fa4..0000000 --- a/example of results/PL_family_WGS_slivar_1664358140/reports/trace.txt +++ /dev/null @@ -1,4 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar -3 00/e6eb69 29539507 Backup COMPLETED 0 2022-09-28 11:42:21.685 9.7s 14ms 5.4% 0 0 122.3 KB 1.5 KB -1 60/eb369a 29539508 WorkflowVersion COMPLETED 0 2022-09-28 11:42:21.744 9.7s 519ms 4.6% 5.2 MB 38.5 MB 151.1 KB 3.3 KB -2 36/8a923b 29539509 slivar COMPLETED 0 2022-09-28 11:42:21.799 17m 40s 17m 31s 95.3% 2.2 GB 2.3 GB 6.5 GB 848.1 KB diff --git a/example of results/PL_family_WGS_slivar_1664358140/res.tsv b/example of results/PL_family_WGS_slivar_1664358140/res.tsv deleted file mode 100644 index e0a1b10..0000000 --- a/example of results/PL_family_WGS_slivar_1664358140/res.tsv +++ /dev/null @@ -1,1009 +0,0 @@ -#mode family_id sample_id chr:pos:ref:alt genotype(sample,dad,mom) AC AF AN BaseQRankSum DB DP ExcessHet FS InbreedingCoeff MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR VQSLOD culprit CSQ cadd_phred gno_non_neuro_af_all gno_non_neuro_af_nfe gno_non_neuro_nhomalt_all gno_non_neuro_nhomalt_nfe highest_impact_order aff_only depths(sample,dad,mom) allele_balance(sample,dad,mom) -aff_only fam_pl C0011JZ chr1:142674001:C:T 1,.,. 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 101,.,. 0.148515,.,. -aff_only fam_pl C0011K2 chr1:142674001:C:T 1,.,. 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 102,.,. 0.0882353,.,. -aff_only fam_pl C0011K3 chr1:142674001:C:T 1,.,. 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 85,.,. 0.0941176,.,. -aff_only fam_pl C0011KA chr1:142674001:C:T 1,.,1 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 128,.,102 0.203125,.,0.0882353 -aff_only fam_pl IP00FNP chr1:142674001:C:T 1,.,1 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 157,.,101 0.273885,.,0.148515 -aff_only fam_pl IP00FNW chr1:142674001:C:T 1,.,. 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.147541,.,. -aff_only fam_pl IP00FNY chr1:142674001:C:T 1,.,. 7 0.318 22 0.31 DB 1223 9.0714 8.045 -0.467 7 0.318 42.32 -2.342 2.86 0.256 1.492 -4.51 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.303041 0.339451 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 153,.,. 0.117647,.,. -aff_only fam_pl C0011JZ chr1:146487361:ACC:* 1,.,. 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.444444,.,. -aff_only fam_pl C0011K2 chr1:146487361:ACC:* 1,.,. 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.153846,.,. -aff_only fam_pl C0011K3 chr1:146487361:ACC:* 1,.,. 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.0810811,.,. -aff_only fam_pl C0011KA chr1:146487361:ACC:* 1,.,1 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,39 0.148148,.,0.153846 -aff_only fam_pl IP00FNP chr1:146487361:ACC:* 1,.,1 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,18 0.419355,.,0.444444 -aff_only fam_pl IP00FNW chr1:146487361:ACC:* 1,.,. 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr1:146487361:ACC:* 1,.,. 7 0.318 22 -0.103 397 20.6 13.198 -0.8858 7 0.318 29.75 1.31 0.69 1.64 1.251 -1.591 MQ -1 -1 -1 -1 -1 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.31746,.,. -aff_only fam_pl C0011JZ chr2:53605544:T:TTTTTA 1,.,. 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.52381,.,. -aff_only fam_pl C0011K2 chr2:53605544:T:TTTTTA 1,.,. 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.516129,.,. -aff_only fam_pl C0011K3 chr2:53605544:T:TTTTTA 1,.,. 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.447368,.,. -aff_only fam_pl C0011KA chr2:53605544:T:TTTTTA 1,.,1 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,31 0.545455,.,0.516129 -aff_only fam_pl IP00FNP chr2:53605544:T:TTTTTA 1,.,1 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,21 0.6,.,0.52381 -aff_only fam_pl IP00FNW chr2:53605544:T:TTTTTA 1,.,. 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.555556,.,. -aff_only fam_pl IP00FNY chr2:53605544:T:TTTTTA 1,.,. 7 0.318 22 0.754 DB 504 9.0714 6.984 -0.4667 7 0.318 60.09 0 21.37 -0.352 0.727 8.51 MQRankSum TTTTA|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.453228 0.357854 2369 819 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,. 0.493151,.,. -aff_only fam_pl C0011JZ chr2:53606631:C:T 1,.,. 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.470588,.,. -aff_only fam_pl C0011K2 chr2:53606631:C:T 1,.,. 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.578947,.,. -aff_only fam_pl C0011K3 chr2:53606631:C:T 1,.,. 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.538462,.,. -aff_only fam_pl C0011KA chr2:53606631:C:T 1,.,1 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,38 0.472222,.,0.578947 -aff_only fam_pl IP00FNP chr2:53606631:C:T 1,.,1 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,51 0.491803,.,0.470588 -aff_only fam_pl IP00FNW chr2:53606631:C:T 1,.,. 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.483871,.,. -aff_only fam_pl IP00FNY chr2:53606631:C:T 1,.,. 7 0.318 22 1.23 DB 519 9.0714 0 -0.4667 7 0.318 60 0 14.71 0.429 0.7 23.52 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.454644 0.358489 2456 857 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 71,.,. 0.577465,.,. -aff_only fam_pl C0011JZ chr2:53611448:T:A 1,.,. 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr2:53611448:T:A 1,.,. 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.613636,.,. -aff_only fam_pl C0011K3 chr2:53611448:T:A 1,.,. 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.617021,.,. -aff_only fam_pl C0011KA chr2:53611448:T:A 1,.,1 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,44 0.558824,.,0.613636 -aff_only fam_pl IP00FNP chr2:53611448:T:A 1,.,1 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 64,.,34 0.4375,.,0.5 -aff_only fam_pl IP00FNW chr2:53611448:T:A 1,.,. 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 58,.,. 0.448276,.,. -aff_only fam_pl IP00FNY chr2:53611448:T:A 1,.,. 7 0.318 22 0 DB 484 9.0714 0.388 -0.4667 7 0.318 60 0 14.87 -0.338 0.726 23.79 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.457699 0.358439 2490 851 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 67,.,. 0.567164,.,. -aff_only fam_pl C0011JZ chr2:55855379:CA:C 1,.,. 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 9,.,. 0.666667,.,. -aff_only fam_pl C0011K2 chr2:55855379:CA:C 1,.,. 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.857143,.,. -aff_only fam_pl C0011K3 chr2:55855379:CA:C 1,.,. 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,. 0.583333,.,. -aff_only fam_pl C0011KA chr2:55855379:CA:C 1,.,1 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,7 0.714286,.,0.857143 -aff_only fam_pl IP00FNP chr2:55855379:CA:C 1,.,1 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 4,.,9 0.25,.,0.666667 -aff_only fam_pl IP00FNW chr2:55855379:CA:C 1,.,. 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 5,.,. 0.8,.,. -aff_only fam_pl IP00FNY chr2:55855379:CA:C 1,.,. 7 0.318 22 0.566 DB 226 5.8108 6.666 -0.3786 6 0.273 59.92 0 7.71 0.366 1.483 5.55 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.581573 0.577764 1048 734 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.428571,.,. -aff_only fam_pl C0011JZ chr2:61475320:CA:C 1,.,. 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.545455,.,. -aff_only fam_pl C0011K2 chr2:61475320:CA:C 1,.,. 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.529412,.,. -aff_only fam_pl C0011K3 chr2:61475320:CA:C 1,.,. 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.545455,.,. -aff_only fam_pl C0011KA chr2:61475320:CA:C 1,.,1 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,17 0.857143,.,0.529412 -aff_only fam_pl IP00FNP chr2:61475320:CA:C 1,.,1 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 8,.,11 0.5,.,0.545455 -aff_only fam_pl IP00FNW chr2:61475320:CA:C 1,.,. 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.428571,.,. -aff_only fam_pl IP00FNY chr2:61475320:CA:C 1,.,. 7 0.318 22 0 DB 252 4.3978 0 -0.2173 7 0.318 57.71 0 9.68 0.199 0.618 1.8 MQRankSum -|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES|||| -1 0.357445 0.346886 139 80 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 5,.,. 0.2,.,. -aff_only fam_pl C0011JZ chr2:65103319:T:C 1,.,. 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.416667,.,. -aff_only fam_pl C0011K2 chr2:65103319:T:C 1,.,. 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.354839,.,. -aff_only fam_pl C0011K3 chr2:65103319:T:C 1,.,. 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.583333,.,. -aff_only fam_pl C0011KA chr2:65103319:T:C 1,.,1 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,31 0.464286,.,0.354839 -aff_only fam_pl IP00FNP chr2:65103319:T:C 1,.,1 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,24 0.638889,.,0.416667 -aff_only fam_pl IP00FNW chr2:65103319:T:C 1,.,. 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.578947,.,. -aff_only fam_pl IP00FNY chr2:65103319:T:C 1,.,. 7 0.318 22 0.267 DB 396 9.0714 6.104 -0.4667 7 0.318 60 0 14.35 -0.821 0.842 24 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| 14.1 0.556663 0.484578 3367 1561 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.543478,.,. -aff_only fam_pl C0011JZ chr2:65103814:A:G 1,.,. 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.387097,.,. -aff_only fam_pl C0011K2 chr2:65103814:A:G 1,.,. 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.413793,.,. -aff_only fam_pl C0011K3 chr2:65103814:A:G 1,.,. 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.454545,.,. -aff_only fam_pl C0011KA chr2:65103814:A:G 1,.,1 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,29 0.565217,.,0.413793 -aff_only fam_pl IP00FNP chr2:65103814:A:G 1,.,1 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,31 0.403226,.,0.387097 -aff_only fam_pl IP00FNW chr2:65103814:A:G 1,.,. 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr2:65103814:A:G 1,.,. 7 0.318 22 -1.192 DB 449 9.0714 3.177 -0.4667 7 0.318 60 0 11.16 -0.024 0.534 23.48 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.506841 0.473258 2723 1490 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.440678,.,. -aff_only fam_pl C0011JZ chr2:65103931:G:GTTT 1,.,. 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.555556,.,. -aff_only fam_pl C0011K2 chr2:65103931:G:GTTT 1,.,. 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.333333,.,. -aff_only fam_pl C0011K3 chr2:65103931:G:GTTT 1,.,. 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.454545,.,. -aff_only fam_pl C0011KA chr2:65103931:G:GTTT 1,.,1 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,36 0.695652,.,0.333333 -aff_only fam_pl IP00FNP chr2:65103931:G:GTTT 1,.,1 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,18 0.571429,.,0.555556 -aff_only fam_pl IP00FNW chr2:65103931:G:GTTT 1,.,. 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.571429,.,. -aff_only fam_pl IP00FNY chr2:65103931:G:GTTT 1,.,. 7 0.318 22 0.179 DB 397 9.0714 2.238 -0.4667 7 0.318 60 0 19.41 -0.356 0.871 8.92 MQRankSum TTT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.509393 0.46758 2515 1338 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.466667,.,. -aff_only fam_pl C0011JZ chr2:65103983:G:A 1,.,. 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,. 0.565217,.,. -aff_only fam_pl C0011K2 chr2:65103983:G:A 1,.,. 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.333333,.,. -aff_only fam_pl C0011K3 chr2:65103983:G:A 1,.,. 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.516129,.,. -aff_only fam_pl C0011KA chr2:65103983:G:A 1,.,1 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,39 0.692308,.,0.333333 -aff_only fam_pl IP00FNP chr2:65103983:G:A 1,.,1 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,23 0.475,.,0.565217 -aff_only fam_pl IP00FNW chr2:65103983:G:A 1,.,. 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.6,.,. -aff_only fam_pl IP00FNY chr2:65103983:G:A 1,.,. 7 0.318 22 -0.904 DB 381 9.0714 7.072 -0.4667 7 0.318 60 0 13.24 -0.244 0.843 24.28 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.504025 0.469158 2647 1431 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.377778,.,. -aff_only fam_pl C0011JZ chr2:65104485:A:G 1,.,. 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.575,.,. -aff_only fam_pl C0011K2 chr2:65104485:A:G 1,.,. 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.619048,.,. -aff_only fam_pl C0011K3 chr2:65104485:A:G 1,.,. 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.543478,.,. -aff_only fam_pl C0011KA chr2:65104485:A:G 1,.,1 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,42 0.324324,.,0.619048 -aff_only fam_pl IP00FNP chr2:65104485:A:G 1,.,1 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,40 0.528302,.,0.575 -aff_only fam_pl IP00FNW chr2:65104485:A:G 1,.,. 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.465116,.,. -aff_only fam_pl IP00FNY chr2:65104485:A:G 1,.,. 7 0.318 22 -1.493 DB 473 9.0714 0 -0.4667 7 0.318 60 0 13.76 0 0.705 23.5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.52367 0.475941 2933 1508 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 58,.,. 0.637931,.,. -aff_only fam_pl C0011JZ chr2:65106350:C:T 1,.,. 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.594595,.,. -aff_only fam_pl C0011K2 chr2:65106350:C:T 1,.,. 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.466667,.,. -aff_only fam_pl C0011K3 chr2:65106350:C:T 1,.,. 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.478261,.,. -aff_only fam_pl C0011KA chr2:65106350:C:T 1,.,1 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,30 0.441176,.,0.466667 -aff_only fam_pl IP00FNP chr2:65106350:C:T 1,.,1 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,37 0.571429,.,0.594595 -aff_only fam_pl IP00FNW chr2:65106350:C:T 1,.,. 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.358974,.,. -aff_only fam_pl IP00FNY chr2:65106350:C:T 1,.,. 7 0.318 22 0.16 DB 462 9.0714 0.869 -0.4667 7 0.318 60 0 13.84 -0.173 0.697 23.74 MQRankSum T|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.527461 0.475917 2999 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.516129,.,. -aff_only fam_pl C0011JZ chr2:65106492:A:G 1,.,. 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.4,.,. -aff_only fam_pl C0011K2 chr2:65106492:A:G 1,.,. 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.387097,.,. -aff_only fam_pl C0011K3 chr2:65106492:A:G 1,.,. 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.4,.,. -aff_only fam_pl C0011KA chr2:65106492:A:G 1,.,1 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,31 0.515152,.,0.387097 -aff_only fam_pl IP00FNP chr2:65106492:A:G 1,.,1 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,30 0.555556,.,0.4 -aff_only fam_pl IP00FNW chr2:65106492:A:G 1,.,. 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.537037,.,. -aff_only fam_pl IP00FNY chr2:65106492:A:G 1,.,. 7 0.318 22 -0.85 DB 446 9.0714 3.167 -0.4667 7 0.318 60 0 13.25 0.09 0.883 23.77 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.528879 0.47651 3011 1513 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.491525,.,. -aff_only fam_pl C0011JZ chr2:65106712:T:TG 1,.,. 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.466667,.,. -aff_only fam_pl C0011K2 chr2:65106712:T:TG 1,.,. 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.482759,.,. -aff_only fam_pl C0011K3 chr2:65106712:T:TG 1,.,. 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.511628,.,. -aff_only fam_pl C0011KA chr2:65106712:T:TG 1,.,1 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,29 0.575,.,0.482759 -aff_only fam_pl IP00FNP chr2:65106712:T:TG 1,.,1 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,30 0.469388,.,0.466667 -aff_only fam_pl IP00FNW chr2:65106712:T:TG 1,.,. 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.53125,.,. -aff_only fam_pl IP00FNY chr2:65106712:T:TG 1,.,. 7 0.318 22 -0.845 DB 422 9.0714 8.562 -0.4667 7 0.318 60.04 0 13.46 -0.241 1.136 8.78 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.552132 0.482733 3298 1553 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.555556,.,. -aff_only fam_pl C0011JZ chr2:65107942:G:A 1,.,. 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.45,.,. -aff_only fam_pl C0011K2 chr2:65107942:G:A 1,.,. 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.531915,.,. -aff_only fam_pl C0011K3 chr2:65107942:G:A 1,.,. 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.44186,.,. -aff_only fam_pl C0011KA chr2:65107942:G:A 1,.,1 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,47 0.55,.,0.531915 -aff_only fam_pl IP00FNP chr2:65107942:G:A 1,.,1 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,20 0.48,.,0.45 -aff_only fam_pl IP00FNW chr2:65107942:G:A 1,.,. 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.333333,.,. -aff_only fam_pl IP00FNY chr2:65107942:G:A 1,.,. 7 0.318 22 1.59 DB 447 9.0714 3.057 -0.4667 7 0.318 60 0 13.29 0.115 0.764 23.72 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.493539 0.469991 2570 1474 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,. 0.493151,.,. -aff_only fam_pl C0011JZ chr2:65108615:T:C 1,.,. 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.580645,.,. -aff_only fam_pl C0011K2 chr2:65108615:T:C 1,.,. 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.411765,.,. -aff_only fam_pl C0011K3 chr2:65108615:T:C 1,.,. 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.5,.,. -aff_only fam_pl C0011KA chr2:65108615:T:C 1,.,1 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,51 0.454545,.,0.411765 -aff_only fam_pl IP00FNP chr2:65108615:T:C 1,.,1 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,31 0.468085,.,0.580645 -aff_only fam_pl IP00FNW chr2:65108615:T:C 1,.,. 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.52381,.,. -aff_only fam_pl IP00FNY chr2:65108615:T:C 1,.,. 7 0.318 22 -1.861 DB 479 9.0714 8.259 -0.4667 7 0.318 60 0 12.78 0.189 0.421 23.99 MQRankSum C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523677 0.476583 2941 1515 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 75,.,. 0.56,.,. -aff_only fam_pl C0011JZ chr2:65109039:A:G 1,.,. 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.488889,.,. -aff_only fam_pl C0011K2 chr2:65109039:A:G 1,.,. 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.318182,.,. -aff_only fam_pl C0011K3 chr2:65109039:A:G 1,.,. 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.548387,.,. -aff_only fam_pl C0011KA chr2:65109039:A:G 1,.,1 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,44 0.583333,.,0.318182 -aff_only fam_pl IP00FNP chr2:65109039:A:G 1,.,1 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,45 0.392157,.,0.488889 -aff_only fam_pl IP00FNW chr2:65109039:A:G 1,.,. 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.490196,.,. -aff_only fam_pl IP00FNY chr2:65109039:A:G 1,.,. 7 0.318 22 -0.843 DB 473 9.0714 2.363 -0.4667 7 0.318 59.96 0 12 0.182 0.638 8.81 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.523857 0.4766 2945 1516 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.514286,.,. -aff_only fam_pl C0011JZ chr2:65388081:TA:T 1,.,. 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.65,.,. -aff_only fam_pl C0011K2 chr2:65388081:TA:T 1,.,. 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.428571,.,. -aff_only fam_pl C0011K3 chr2:65388081:TA:T 1,.,. 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.535714,.,. -aff_only fam_pl C0011KA chr2:65388081:TA:T 1,.,1 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,21 0.692308,.,0.428571 -aff_only fam_pl IP00FNP chr2:65388081:TA:T 1,.,1 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,20 0.5,.,0.65 -aff_only fam_pl IP00FNW chr2:65388081:TA:T 1,.,. 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.588235,.,. -aff_only fam_pl IP00FNY chr2:65388081:TA:T 1,.,. 7 0.318 22 -0.396 DB 291 9.0714 15.397 -0.6923 9 0.409 59.33 0 19.79 0.534 1.689 6.12 MQRankSum -|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES|||| -1 0.505715 0.526476 2246 1563 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.586207,.,. -aff_only fam_pl C0011JZ chr2:65525953:A:ATT 1,.,. 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 6,.,. 1,.,. -aff_only fam_pl C0011K2 chr2:65525953:A:ATT 1,.,. 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 0.9,.,. -aff_only fam_pl C0011K3 chr2:65525953:A:ATT 1,.,. 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 1,.,. -aff_only fam_pl C0011KA chr2:65525953:A:ATT 1,.,1 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,10 0.9,.,0.9 -aff_only fam_pl IP00FNP chr2:65525953:A:ATT 1,.,1 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,6 1,.,1 -aff_only fam_pl IP00FNW chr2:65525953:A:ATT 1,.,. 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 1,.,. 1,.,. -aff_only fam_pl IP00FNY chr2:65525953:A:ATT 1,.,. 7 0.318 22 -0.095 DB 280 4.4261 1.965 -0.2222 7 0.318 56.39 0 15.91 -0.183 1.019 -0.3518 MQRankSum TT|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.251169 0.27406 427 318 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.636364,.,. -aff_only fam_pl C0011JZ chr2:67234368:TA:T 1,.,. 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.647059,.,. -aff_only fam_pl C0011K2 chr2:67234368:TA:T 1,.,. 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.619048,.,. -aff_only fam_pl C0011K3 chr2:67234368:TA:T 1,.,. 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,. 0.384615,.,. -aff_only fam_pl C0011KA chr2:67234368:TA:T 1,.,1 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,21 0.285714,.,0.619048 -aff_only fam_pl IP00FNP chr2:67234368:TA:T 1,.,1 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,17 0.5,.,0.647059 -aff_only fam_pl IP00FNW chr2:67234368:TA:T 1,.,. 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.470588,.,. -aff_only fam_pl IP00FNY chr2:67234368:TA:T 1,.,. 7 0.318 22 -0.645 DB 230 9.0714 3.637 -0.5169 7 0.318 60 0 7.84 -0.566 0.397 7.87 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.538314 0.539987 761 470 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.181818,.,. -aff_only fam_pl C0011JZ chr2:69028241:T:TA 1,.,. 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.722222,.,. -aff_only fam_pl C0011K2 chr2:69028241:T:TA 1,.,. 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.526316,.,. -aff_only fam_pl C0011K3 chr2:69028241:T:TA 1,.,. 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.545455,.,. -aff_only fam_pl C0011KA chr2:69028241:T:TA 1,.,1 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,38 0.423077,.,0.526316 -aff_only fam_pl IP00FNP chr2:69028241:T:TA 1,.,1 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,36 0.571429,.,0.722222 -aff_only fam_pl IP00FNW chr2:69028241:T:TA 1,.,. 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.472222,.,. -aff_only fam_pl IP00FNY chr2:69028241:T:TA 1,.,. 7 0.318 22 -0.852 DB 456 9.0714 4.856 -0.4667 7 0.318 60.04 0 12.69 -0.452 0.47 8.44 MQRankSum A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951||||| -1 0.474334 0.504923 2296 1651 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.54386,.,. -aff_only fam_pl C0011JZ chr2:71706563:G:C 1,.,. 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.461538,.,. -aff_only fam_pl C0011K2 chr2:71706563:G:C 1,.,. 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.387097,.,. -aff_only fam_pl C0011K3 chr2:71706563:G:C 1,.,. 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.368421,.,. -aff_only fam_pl C0011KA chr2:71706563:G:C 1,.,1 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,31 0.310345,.,0.387097 -aff_only fam_pl IP00FNP chr2:71706563:G:C 1,.,1 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,26 0.454545,.,0.461538 -aff_only fam_pl IP00FNW chr2:71706563:G:C 1,.,. 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.372093,.,. -aff_only fam_pl IP00FNY chr2:71706563:G:C 1,.,. 7 0.318 22 -1.192 DB 390 9.0714 8.279 -0.4667 7 0.318 60 0 9.19 -0.344 1 24.29 MQRankSum C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1||| -1 0.340463 0.411795 1286 1098 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.395349,.,. -aff_only fam_pl C0011JZ chr2:114352135:G:A 1,.,. 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.214286,.,. -aff_only fam_pl C0011K2 chr2:114352135:G:A 1,.,. 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,. 0.215385,.,. -aff_only fam_pl C0011K3 chr2:114352135:G:A 1,.,. 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.14,.,. -aff_only fam_pl C0011KA chr2:114352135:G:A 1,.,1 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,65 0.20339,.,0.215385 -aff_only fam_pl IP00FNP chr2:114352135:G:A 1,.,1 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,42 0.125,.,0.214286 -aff_only fam_pl IP00FNW chr2:114352135:G:A 1,.,. 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.170213,.,. -aff_only fam_pl IP00FNY chr2:114352135:G:A 1,.,. 7 0.318 22 -0.216 DB 554 9.0714 49.345 -0.4741 7 0.318 42.7 -3.311 1.79 -0.866 4.068 -32.31 SOR A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES|||| -1 0.092277 0.0950659 0 0 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 60,.,. 0.133333,.,. -aff_only fam_pl C0011JZ chr7:628664:A:G 1,.,. 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.0952381,.,. -aff_only fam_pl C0011K2 chr7:628664:A:G 1,.,. 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 15,.,. 0.133333,.,. -aff_only fam_pl C0011K3 chr7:628664:A:G 1,.,. 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.116279,.,. -aff_only fam_pl C0011KA chr7:628664:A:G 1,.,1 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,15 0.0833333,.,0.133333 -aff_only fam_pl IP00FNP chr7:628664:A:G 1,.,1 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 58,.,21 0.206897,.,0.0952381 -aff_only fam_pl IP00FNW chr7:628664:A:G 1,.,. 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.176471,.,. -aff_only fam_pl IP00FNY chr7:628664:A:G 1,.,. 7 0.318 22 -1.067 DB 545 9.0714 0.653 -0.5133 7 0.318 54.65 -4.686 2.21 1.18 0.58 -3.475 MQ G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1||| -1 0.185854 0.188696 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.142857,.,. -aff_only fam_pl C0011JZ chr7:143492092:C:T 1,.,. 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.208333,.,. -aff_only fam_pl C0011K2 chr7:143492092:C:T 1,.,. 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.171429,.,. -aff_only fam_pl C0011K3 chr7:143492092:C:T 1,.,. 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.2,.,. -aff_only fam_pl C0011KA chr7:143492092:C:T 1,.,1 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,35 0.222222,.,0.171429 -aff_only fam_pl IP00FNP chr7:143492092:C:T 1,.,1 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,24 0.482759,.,0.208333 -aff_only fam_pl IP00FNW chr7:143492092:C:T 1,.,. 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.166667,.,. -aff_only fam_pl IP00FNY chr7:143492092:C:T 1,.,. 7 0.318 22 1.06 299 9.0714 0 -0.5172 7 0.318 39.44 0 5.19 0.319 0.346 -4.537 MQ T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene|||||| -1 0.0307973 0.0267106 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.214286,.,. -aff_only fam_pl C0011JZ chr7:143897347:A:G 1,.,. 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.16129,.,. -aff_only fam_pl C0011K2 chr7:143897347:A:G 1,.,. 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.214286,.,. -aff_only fam_pl C0011K3 chr7:143897347:A:G 1,.,. 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.222222,.,. -aff_only fam_pl C0011KA chr7:143897347:A:G 1,.,1 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,28 0.310345,.,0.214286 -aff_only fam_pl IP00FNP chr7:143897347:A:G 1,.,1 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,31 0.189189,.,0.16129 -aff_only fam_pl IP00FNW chr7:143897347:A:G 1,.,. 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.166667,.,. -aff_only fam_pl IP00FNY chr7:143897347:A:G 1,.,. 7 0.318 22 0 DB 309 9.0714 85.285 -0.5174 7 0.318 33.37 1.79 4.24 -0.238 6.827 -97.48 SOR G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.26168 0.250156 55 37 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.244444,.,. -aff_only fam_pl C0011JZ chr7:143901937:C:T 1,.,. 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.190476,.,. -aff_only fam_pl C0011K2 chr7:143901937:C:T 1,.,. 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 85,.,. 0.164706,.,. -aff_only fam_pl C0011K3 chr7:143901937:C:T 1,.,. 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 98,.,. 0.122449,.,. -aff_only fam_pl C0011KA chr7:143901937:C:T 1,.,1 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,85 0.291667,.,0.164706 -aff_only fam_pl IP00FNP chr7:143901937:C:T 1,.,1 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,63 0.145455,.,0.190476 -aff_only fam_pl IP00FNW chr7:143901937:C:T 1,.,. 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.196078,.,. -aff_only fam_pl IP00FNY chr7:143901937:C:T 1,.,. 7 0.318 22 -0.501 670 9.0714 4.325 -0.5172 7 0.318 27.51 0.158 3.03 0.108 0.991 -10.21 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.134101 0.103901 9 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.344262,.,. -aff_only fam_pl C0011JZ chr7:143901963:G:A 1,.,. 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.175,.,. -aff_only fam_pl C0011K2 chr7:143901963:G:A 1,.,. 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 101,.,. 0.148515,.,. -aff_only fam_pl C0011K3 chr7:143901963:G:A 1,.,. 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 116,.,. 0.103448,.,. -aff_only fam_pl C0011KA chr7:143901963:G:A 1,.,1 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,101 0.306452,.,0.148515 -aff_only fam_pl IP00FNP chr7:143901963:G:A 1,.,1 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 86,.,80 0.139535,.,0.175 -aff_only fam_pl IP00FNW chr7:143901963:G:A 1,.,. 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 91,.,. 0.131868,.,. -aff_only fam_pl IP00FNY chr7:143901963:G:A 1,.,. 7 0.318 22 1.5 DB 878 9.0714 1.528 -0.4643 7 0.318 27.67 0.017 2.73 0.773 0.67 -10.09 MQ A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.182612 0.148653 11 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 110,.,. 0.345455,.,. -aff_only fam_pl C0011JZ chr7:143904241:A:G 1,.,. 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.231884,.,. -aff_only fam_pl C0011K2 chr7:143904241:A:G 1,.,. 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.140351,.,. -aff_only fam_pl C0011K3 chr7:143904241:A:G 1,.,. 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 84,.,. 0.178571,.,. -aff_only fam_pl C0011KA chr7:143904241:A:G 1,.,1 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,57 0.357143,.,0.140351 -aff_only fam_pl IP00FNP chr7:143904241:A:G 1,.,1 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 95,.,69 0.221053,.,0.231884 -aff_only fam_pl IP00FNW chr7:143904241:A:G 1,.,. 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 74,.,. 0.216216,.,. -aff_only fam_pl IP00FNY chr7:143904241:A:G 1,.,. 7 0.318 22 0.018 DB 701 9.0714 11.359 -0.5172 7 0.318 32.63 -0.299 3.25 -1.483 1.497 -9.891 MQ G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.274984 0.262682 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 100,.,. 0.13,.,. -aff_only fam_pl C0011JZ chr7:143989050:C:T 1,.,. 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.192308,.,. -aff_only fam_pl C0011K2 chr7:143989050:C:T 1,.,. 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,. 0.214286,.,. -aff_only fam_pl C0011K3 chr7:143989050:C:T 1,.,. 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.310345,.,. -aff_only fam_pl C0011KA chr7:143989050:C:T 1,.,1 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,14 0.4375,.,0.214286 -aff_only fam_pl IP00FNP chr7:143989050:C:T 1,.,1 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,26 0.266667,.,0.192308 -aff_only fam_pl IP00FNW chr7:143989050:C:T 1,.,. 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.285714,.,. -aff_only fam_pl IP00FNY chr7:143989050:C:T 1,.,. 7 0.318 22 0 DB 282 9.0714 7.071 -0.4667 7 0.318 26.71 0 4.95 -0.532 0.952 -10.45 MQ T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.300719 0.280411 8 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.243902,.,. -aff_only fam_pl C0011JZ chr7:143989124:T:C 1,.,. 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.333333,.,. -aff_only fam_pl C0011K2 chr7:143989124:T:C 1,.,. 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.230769,.,. -aff_only fam_pl C0011K3 chr7:143989124:T:C 1,.,. 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.291667,.,. -aff_only fam_pl C0011KA chr7:143989124:T:C 1,.,1 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,39 0.461538,.,0.230769 -aff_only fam_pl IP00FNP chr7:143989124:T:C 1,.,1 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,33 0.294118,.,0.333333 -aff_only fam_pl IP00FNW chr7:143989124:T:C 1,.,. 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.277778,.,. -aff_only fam_pl IP00FNY chr7:143989124:T:C 1,.,. 7 0.318 22 -2.573 DB 437 9.0714 13.386 -0.5172 7 0.318 25.57 0 5.87 -0.174 1.348 -14 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1||| -1 0.31982 0.305004 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.372549,.,. -aff_only fam_pl C0011JZ chr7:144659042:TATACAC:T 1,.,. 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.333333,.,. -aff_only fam_pl C0011K2 chr7:144659042:TATACAC:T 1,.,. 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.222222,.,. -aff_only fam_pl C0011K3 chr7:144659042:TATACAC:T 1,.,. 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.375,.,. -aff_only fam_pl C0011KA chr7:144659042:TATACAC:T 1,.,1 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,18 0.631579,.,0.222222 -aff_only fam_pl IP00FNP chr7:144659042:TATACAC:T 1,.,1 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,21 0.181818,.,0.333333 -aff_only fam_pl IP00FNW chr7:144659042:TATACAC:T 1,.,. 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.545455,.,. -aff_only fam_pl IP00FNY chr7:144659042:TATACAC:T 1,.,. 7 0.318 22 0 DB 313 9.0714 6.166 -0.5298 7 0.318 60.14 0 7.61 0.794 0.752 7.17 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0591229 0.0532034 13 5 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.222222,.,. -aff_only fam_pl C0011JZ chr7:146603134:G:A 1,.,. 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.6,.,. -aff_only fam_pl C0011K2 chr7:146603134:G:A 1,.,. 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.446809,.,. -aff_only fam_pl C0011K3 chr7:146603134:G:A 1,.,. 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.660714,.,. -aff_only fam_pl C0011KA chr7:146603134:G:A 1,.,1 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,47 0.452381,.,0.446809 -aff_only fam_pl IP00FNP chr7:146603134:G:A 1,.,1 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,30 0.5,.,0.6 -aff_only fam_pl IP00FNW chr7:146603134:G:A 1,.,. 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.634146,.,. -aff_only fam_pl IP00FNY chr7:146603134:G:A 1,.,. 7 0.318 22 0.052 DB 478 9.0714 5.008 -0.4667 7 0.318 53.32 0.189 15.41 0.593 0.489 -1.811 MQ A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0395233 0.0491249 12 10 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.564516,.,. -aff_only fam_pl C0011JZ chr7:146655898:C:G 1,.,. 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.592593,.,. -aff_only fam_pl C0011K2 chr7:146655898:C:G 1,.,. 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.583333,.,. -aff_only fam_pl C0011K3 chr7:146655898:C:G 1,.,. 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.452381,.,. -aff_only fam_pl C0011KA chr7:146655898:C:G 1,.,1 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,36 0.444444,.,0.583333 -aff_only fam_pl IP00FNP chr7:146655898:C:G 1,.,1 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,27 0.566038,.,0.592593 -aff_only fam_pl IP00FNW chr7:146655898:C:G 1,.,. 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.576271,.,. -aff_only fam_pl IP00FNY chr7:146655898:C:G 1,.,. 7 0.318 22 1.18 448 9.0714 1.828 -0.4667 7 0.318 60 0 14.43 0.683 0.819 21.97 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 71,.,. 0.408451,.,. -aff_only fam_pl C0011JZ chr7:146778675:T:TTG 1,.,. 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,. 0.333333,.,. -aff_only fam_pl C0011K2 chr7:146778675:T:TTG 1,.,. 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 15,.,. 0.6,.,. -aff_only fam_pl C0011K3 chr7:146778675:T:TTG 1,.,. 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.647059,.,. -aff_only fam_pl C0011KA chr7:146778675:T:TTG 1,.,1 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 4,.,15 1,.,0.6 -aff_only fam_pl IP00FNP chr7:146778675:T:TTG 1,.,1 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 8,.,12 0.375,.,0.333333 -aff_only fam_pl IP00FNW chr7:146778675:T:TTG 1,.,. 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,. 1,.,. -aff_only fam_pl IP00FNY chr7:146778675:T:TTG 1,.,. 7 0.318 22 -0.231 DB 332 11.8014 5.311 -0.5714 7 0.318 59.84 0 17.37 -0.222 0.642 6.77 MQRankSum TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES|||| -1 0.0743969 0.051922 83 14 39 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.714286,.,. -aff_only fam_pl C0011JZ chr7:146790164:C:CAT 1,.,. 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr7:146790164:C:CAT 1,.,. 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 1,.,. -aff_only fam_pl C0011K3 chr7:146790164:C:CAT 1,.,. 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 1,.,. -aff_only fam_pl C0011KA chr7:146790164:C:CAT 1,.,1 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,18 0.448276,.,1 -aff_only fam_pl IP00FNP chr7:146790164:C:CAT 1,.,1 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,26 0.947368,.,0.5 -aff_only fam_pl IP00FNW chr7:146790164:C:CAT 1,.,. 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,. 0.9375,.,. -aff_only fam_pl IP00FNY chr7:146790164:C:CAT 1,.,. 7 0.318 22 0 DB 452 3.6798 8.604 -0.1579 7 0.318 59.87 0 29.2 0.461 0.459 5.58 MQRankSum AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.0176655 0.0213255 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.961538,.,. -aff_only fam_pl C0011JZ chr7:146834965:G:GTAGA 1,.,. 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,. 1,.,. -aff_only fam_pl C0011K2 chr7:146834965:G:GTAGA 1,.,. 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.571429,.,. -aff_only fam_pl C0011K3 chr7:146834965:G:GTAGA 1,.,. 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.571429,.,. -aff_only fam_pl C0011KA chr7:146834965:G:GTAGA 1,.,1 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,28 0.592593,.,0.571429 -aff_only fam_pl IP00FNP chr7:146834965:G:GTAGA 1,.,1 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,16 0.28125,.,1 -aff_only fam_pl IP00FNW chr7:146834965:G:GTAGA 1,.,. 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.516129,.,. -aff_only fam_pl IP00FNY chr7:146834965:G:GTAGA 1,.,. 7 0.318 22 0.126 DB 475 9.3779 8.071 -0.4667 7 0.318 60.28 0.905 22.79 0.714 0.948 1.87 FS TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.223366 0.21519 457 274 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.464286,.,. -aff_only fam_pl C0011JZ chr7:146944250:A:G 1,.,. 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.47619,.,. -aff_only fam_pl C0011K2 chr7:146944250:A:G 1,.,. 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.627907,.,. -aff_only fam_pl C0011K3 chr7:146944250:A:G 1,.,. 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.567568,.,. -aff_only fam_pl C0011KA chr7:146944250:A:G 1,.,1 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,43 0.6,.,0.627907 -aff_only fam_pl IP00FNP chr7:146944250:A:G 1,.,1 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,42 0.609756,.,0.47619 -aff_only fam_pl IP00FNW chr7:146944250:A:G 1,.,. 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.42,.,. -aff_only fam_pl IP00FNY chr7:146944250:A:G 1,.,. 7 0.318 22 -0.356 450 9.0714 5.792 -0.4667 7 0.318 60 0 14.15 0.214 0.52 22.12 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.385714,.,. -aff_only fam_pl C0011JZ chr7:146983589:C:T 1,.,. 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.459459,.,. -aff_only fam_pl C0011K2 chr7:146983589:C:T 1,.,. 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.631579,.,. -aff_only fam_pl C0011K3 chr7:146983589:C:T 1,.,. 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.431818,.,. -aff_only fam_pl C0011KA chr7:146983589:C:T 1,.,1 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,38 0.565217,.,0.631579 -aff_only fam_pl IP00FNP chr7:146983589:C:T 1,.,1 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,37 0.491228,.,0.459459 -aff_only fam_pl IP00FNW chr7:146983589:C:T 1,.,. 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.5375,.,. -aff_only fam_pl IP00FNY chr7:146983589:C:T 1,.,. 7 0.318 22 2.36 DB 508 9.0714 4.61 -0.4667 7 0.318 60 0 14.61 0.217 0.552 23.44 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0140439 0.0185213 4 4 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 85,.,. 0.541176,.,. -aff_only fam_pl C0011JZ chr7:147053066:C:T 1,.,. 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.457143,.,. -aff_only fam_pl C0011K2 chr7:147053066:C:T 1,.,. 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.428571,.,. -aff_only fam_pl C0011K3 chr7:147053066:C:T 1,.,. 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.596154,.,. -aff_only fam_pl C0011KA chr7:147053066:C:T 1,.,1 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,56 0.576923,.,0.428571 -aff_only fam_pl IP00FNP chr7:147053066:C:T 1,.,1 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,35 0.315789,.,0.457143 -aff_only fam_pl IP00FNW chr7:147053066:C:T 1,.,. 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.40678,.,. -aff_only fam_pl IP00FNY chr7:147053066:C:T 1,.,. 7 0.318 22 0 462 9.0714 0.839 -0.4667 7 0.318 59.94 0 12.1 0.836 0.766 6.9 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 4.705e-05 0 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.380952,.,. -aff_only fam_pl C0011JZ chr7:147063869:GCACGCA:G 1,.,. 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.53125,.,. -aff_only fam_pl C0011K2 chr7:147063869:GCACGCA:G 1,.,. 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.366667,.,. -aff_only fam_pl C0011K3 chr7:147063869:GCACGCA:G 1,.,. 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.594595,.,. -aff_only fam_pl C0011KA chr7:147063869:GCACGCA:G 1,.,1 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,30 0.56,.,0.366667 -aff_only fam_pl IP00FNP chr7:147063869:GCACGCA:G 1,.,1 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,32 0.590909,.,0.53125 -aff_only fam_pl IP00FNW chr7:147063869:GCACGCA:G 1,.,. 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.425532,.,. -aff_only fam_pl IP00FNY chr7:147063869:GCACGCA:G 1,.,. 7 0.318 22 0.785 404 6.4503 21.408 -0.3167 7 0.318 60.48 1.34 16.48 -0.235 0.848 -0.7725 MQ -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0303613 0.0327977 9 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,. 1,.,. -aff_only fam_pl C0011JZ chr7:147067882:G:T 1,.,. 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.675676,.,. -aff_only fam_pl C0011K2 chr7:147067882:G:T 1,.,. 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.46,.,. -aff_only fam_pl C0011K3 chr7:147067882:G:T 1,.,. 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.534884,.,. -aff_only fam_pl C0011KA chr7:147067882:G:T 1,.,1 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,50 0.395833,.,0.46 -aff_only fam_pl IP00FNP chr7:147067882:G:T 1,.,1 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,37 0.491525,.,0.675676 -aff_only fam_pl IP00FNW chr7:147067882:G:T 1,.,. 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,. 0.509091,.,. -aff_only fam_pl IP00FNY chr7:147067882:G:T 1,.,. 7 0.318 22 0.49 DB 499 9.0714 1.241 -0.4667 7 0.318 60 0 14.04 -0.477 0.785 23.37 MQRankSum T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0155809 0.0210874 6 6 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 72,.,. 0.486111,.,. -aff_only fam_pl C0011JZ chr7:147118677:C:CTGTGTG 1,.,. 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,. 1,.,. -aff_only fam_pl C0011K2 chr7:147118677:C:CTGTGTG 1,.,. 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,. 1,.,. -aff_only fam_pl C0011K3 chr7:147118677:C:CTGTGTG 1,.,. 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 15,.,. 1,.,. -aff_only fam_pl C0011KA chr7:147118677:C:CTGTGTG 1,.,1 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 9,.,12 1,.,1 -aff_only fam_pl IP00FNP chr7:147118677:C:CTGTGTG 1,.,1 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,19 1,.,1 -aff_only fam_pl IP00FNW chr7:147118677:C:CTGTGTG 1,.,. 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 1,.,. -aff_only fam_pl IP00FNY chr7:147118677:C:CTGTGTG 1,.,. 7 0.318 22 0 DB 481 3.2222 3.536 -0.1 7 0.318 60.13 0 28.73 -0.114 0.891 8.31 MQRankSum TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.444444,.,. -aff_only fam_pl C0011JZ chr7:147124964:T:G 1,.,. 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.5625,.,. -aff_only fam_pl C0011K2 chr7:147124964:T:G 1,.,. 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.410256,.,. -aff_only fam_pl C0011K3 chr7:147124964:T:G 1,.,. 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.611111,.,. -aff_only fam_pl C0011KA chr7:147124964:T:G 1,.,1 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,39 0.658537,.,0.410256 -aff_only fam_pl IP00FNP chr7:147124964:T:G 1,.,1 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,32 0.538462,.,0.5625 -aff_only fam_pl IP00FNW chr7:147124964:T:G 1,.,. 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.566038,.,. -aff_only fam_pl IP00FNY chr7:147124964:T:G 1,.,. 7 0.318 22 0 DB 472 9.0714 5.858 -0.4667 7 0.318 60 0 14.66 0.19 1.007 23.86 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0221218 0.0290963 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 76,.,. 0.407895,.,. -aff_only fam_pl C0011JZ chr7:147128097:G:A 1,.,. 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.48,.,. -aff_only fam_pl C0011K2 chr7:147128097:G:A 1,.,. 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.567568,.,. -aff_only fam_pl C0011K3 chr7:147128097:G:A 1,.,. 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.473684,.,. -aff_only fam_pl C0011KA chr7:147128097:G:A 1,.,1 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,37 0.433333,.,0.567568 -aff_only fam_pl IP00FNP chr7:147128097:G:A 1,.,1 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,25 0.684211,.,0.48 -aff_only fam_pl IP00FNW chr7:147128097:G:A 1,.,. 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.512821,.,. -aff_only fam_pl IP00FNY chr7:147128097:G:A 1,.,. 7 0.318 22 1.31 DB 424 9.0714 0.963 -0.4667 7 0.318 59.94 0 13.57 1.08 0.604 8.18 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.12109 0.161241 180 163 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.377358,.,. -aff_only fam_pl C0011JZ chr7:147145574:G:GTA 1,.,. 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.424242,.,. -aff_only fam_pl C0011K2 chr7:147145574:G:GTA 1,.,. 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr7:147145574:G:GTA 1,.,. 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.457143,.,. -aff_only fam_pl C0011KA chr7:147145574:G:GTA 1,.,1 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,26 0.409091,.,0.5 -aff_only fam_pl IP00FNP chr7:147145574:G:GTA 1,.,1 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,33 0.513514,.,0.424242 -aff_only fam_pl IP00FNW chr7:147145574:G:GTA 1,.,. 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.352941,.,. -aff_only fam_pl IP00FNY chr7:147145574:G:GTA 1,.,. 7 0.318 22 0.329 DB 472 20.6 11.925 -0.8333 7 0.318 60.18 0 11.09 0.58 0.813 5.5 MQRankSum TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.216085 0.241488 193 130 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.306452,.,. -aff_only fam_pl C0011JZ chr7:147157874:T:G 1,.,. 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.407407,.,. -aff_only fam_pl C0011K2 chr7:147157874:T:G 1,.,. 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.638889,.,. -aff_only fam_pl C0011K3 chr7:147157874:T:G 1,.,. 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.477273,.,. -aff_only fam_pl C0011KA chr7:147157874:T:G 1,.,1 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,36 0.580645,.,0.638889 -aff_only fam_pl IP00FNP chr7:147157874:T:G 1,.,1 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,27 0.553571,.,0.407407 -aff_only fam_pl IP00FNW chr7:147157874:T:G 1,.,. 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.587302,.,. -aff_only fam_pl IP00FNY chr7:147157874:T:G 1,.,. 7 0.318 22 -0.968 DB 471 9.0714 0.407 -0.4667 7 0.318 60 0 15.84 0.27 0.742 23.52 MQRankSum G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0148552 0.0195215 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,. 0.584615,.,. -aff_only fam_pl C0011JZ chr7:147170359:G:A 1,.,. 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.555556,.,. -aff_only fam_pl C0011K2 chr7:147170359:G:A 1,.,. 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.555556,.,. -aff_only fam_pl C0011K3 chr7:147170359:G:A 1,.,. 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.486486,.,. -aff_only fam_pl C0011KA chr7:147170359:G:A 1,.,1 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,36 0.357143,.,0.555556 -aff_only fam_pl IP00FNP chr7:147170359:G:A 1,.,1 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,27 0.446154,.,0.555556 -aff_only fam_pl IP00FNW chr7:147170359:G:A 1,.,. 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.528302,.,. -aff_only fam_pl IP00FNY chr7:147170359:G:A 1,.,. 7 0.318 22 1.03 DB 466 9.0714 0.402 -0.4667 7 0.318 60 0 13.32 0.547 0.737 23.42 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.129082 0.16696 204 185 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 79,.,. 0.443038,.,. -aff_only fam_pl C0011JZ chr7:147183978:T:C 1,.,. 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.448276,.,. -aff_only fam_pl C0011K2 chr7:147183978:T:C 1,.,. 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr7:147183978:T:C 1,.,. 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.62069,.,. -aff_only fam_pl C0011KA chr7:147183978:T:C 1,.,1 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,36 0.657143,.,0.5 -aff_only fam_pl IP00FNP chr7:147183978:T:C 1,.,1 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,29 0.422222,.,0.448276 -aff_only fam_pl IP00FNW chr7:147183978:T:C 1,.,. 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.319149,.,. -aff_only fam_pl IP00FNY chr7:147183978:T:C 1,.,. 7 0.318 22 -1.659 DB 419 9.0714 4.886 -0.4667 7 0.318 59.59 0 13.36 -0.822 0.468 4.37 MQRankSum C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.13837 0.175109 200 181 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.387755,.,. -aff_only fam_pl C0011JZ chr7:147191560:C:CAAAAA 1,.,. 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 4,.,. 1,.,. -aff_only fam_pl C0011K2 chr7:147191560:C:CAAAAA 1,.,. 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,. 1,.,. -aff_only fam_pl C0011K3 chr7:147191560:C:CAAAAA 1,.,. 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 1,.,. -aff_only fam_pl C0011KA chr7:147191560:C:CAAAAA 1,.,1 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 6,.,3 1,.,1 -aff_only fam_pl IP00FNP chr7:147191560:C:CAAAAA 1,.,1 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 1,.,4 1,.,1 -aff_only fam_pl IP00FNW chr7:147191560:C:CAAAAA 1,.,. 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,. 1,.,. -aff_only fam_pl IP00FNY chr7:147191560:C:CAAAAA 1,.,. 7 0.318 22 0 DB 288 3.2222 2.68 -0.1 7 0.318 60.07 1.27 35.92 -0.14 0.356 0.871 QD AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.160172 0.157468 287 172 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,. 0.5,.,. -aff_only fam_pl C0011JZ chr7:147199809:ATG:A 1,.,. 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.590909,.,. -aff_only fam_pl C0011K2 chr7:147199809:ATG:A 1,.,. 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.363636,.,. -aff_only fam_pl C0011K3 chr7:147199809:ATG:A 1,.,. 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.52381,.,. -aff_only fam_pl C0011KA chr7:147199809:ATG:A 1,.,1 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,22 0.64,.,0.363636 -aff_only fam_pl IP00FNP chr7:147199809:ATG:A 1,.,1 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,22 0.375,.,0.590909 -aff_only fam_pl IP00FNW chr7:147199809:ATG:A 1,.,. 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.296296,.,. -aff_only fam_pl IP00FNY chr7:147199809:ATG:A 1,.,. 7 0.318 22 0.335 DB 418 9.0714 0 -0.4667 7 0.318 60.04 0 12.39 0 0.721 8.85 MQRankSum -|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.142121 0.168577 201 165 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.44186,.,. -aff_only fam_pl C0011JZ chr7:147205999:G:A 1,.,. 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.454545,.,. -aff_only fam_pl C0011K2 chr7:147205999:G:A 1,.,. 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.424242,.,. -aff_only fam_pl C0011K3 chr7:147205999:G:A 1,.,. 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.560976,.,. -aff_only fam_pl C0011KA chr7:147205999:G:A 1,.,1 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,33 0.391304,.,0.424242 -aff_only fam_pl IP00FNP chr7:147205999:G:A 1,.,1 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,33 0.480769,.,0.454545 -aff_only fam_pl IP00FNW chr7:147205999:G:A 1,.,. 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.534884,.,. -aff_only fam_pl IP00FNY chr7:147205999:G:A 1,.,. 7 0.318 22 1.45 DB 479 9.0714 3.472 -0.4667 7 0.318 60 0 13.55 0.092 0.76 23.44 MQRankSum A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1||| -1 0.0210274 0.027027 5 5 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 92,.,. 0.48913,.,. -aff_only fam_pl C0011JZ chr7:152103755:G:A 1,.,. 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.107143,.,. -aff_only fam_pl C0011K2 chr7:152103755:G:A 1,.,. 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.190476,.,. -aff_only fam_pl C0011K3 chr7:152103755:G:A 1,.,. 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.136364,.,. -aff_only fam_pl C0011KA chr7:152103755:G:A 1,.,1 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,42 0.186047,.,0.190476 -aff_only fam_pl IP00FNP chr7:152103755:G:A 1,.,1 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,28 0.338983,.,0.107143 -aff_only fam_pl IP00FNW chr7:152103755:G:A 1,.,. 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.119048,.,. -aff_only fam_pl IP00FNY chr7:152103755:G:A 1,.,. 7 0.318 22 0.796 DB 534 9.0714 12.11 -0.4567 7 0.318 55.8 -5.587 5.87 2.02 0.643 -2.653 MQ A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726||||| -1 -1 -1 -1 -1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 83,.,. 0.445783,.,. -aff_only fam_pl C0011JZ chr9:45645893:C:A 1,.,. 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,. 0.173913,.,. -aff_only fam_pl C0011K2 chr9:45645893:C:A 1,.,. 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.142857,.,. -aff_only fam_pl C0011K3 chr9:45645893:C:A 1,.,. 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.119048,.,. -aff_only fam_pl C0011KA chr9:45645893:C:A 1,.,1 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,28 0.263158,.,0.142857 -aff_only fam_pl IP00FNP chr9:45645893:C:A 1,.,1 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 58,.,23 0.258621,.,0.173913 -aff_only fam_pl IP00FNW chr9:45645893:C:A 1,.,. 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.244898,.,. -aff_only fam_pl IP00FNY chr9:45645893:C:A 1,.,. 7 0.318 22 -0.248 486 9.0714 39.551 -0.4675 7 0.318 37.36 -1.297 2.68 1.44 2.488 -23.11 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0477956 0.0522528 2 2 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 77,.,. 0.12987,.,. -aff_only fam_pl C0011JZ chr9:69791969:G:C 1,.,. 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.195652,.,. -aff_only fam_pl C0011K2 chr9:69791969:G:C 1,.,. 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.0851064,.,. -aff_only fam_pl C0011K3 chr9:69791969:G:C 1,.,. 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.102041,.,. -aff_only fam_pl C0011KA chr9:69791969:G:C 1,.,1 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,47 0.147059,.,0.0851064 -aff_only fam_pl IP00FNP chr9:69791969:G:C 1,.,1 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,46 0.145833,.,0.195652 -aff_only fam_pl IP00FNW chr9:69791969:G:C 1,.,. 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.2,.,. -aff_only fam_pl IP00FNY chr9:69791969:G:C 1,.,. 7 0.318 22 0.67 DB 571 9.0714 0 -0.4585 7 0.318 31.18 -1.009 1.12 0.097 0.65 -8.379 MQ C|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.12686 0.146961 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 91,.,. 0.131868,.,. -aff_only fam_pl C0011JZ chr9:141127790:AG:A 1,.,. 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.238095,.,. -aff_only fam_pl C0011K2 chr9:141127790:AG:A 1,.,. 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.111111,.,. -aff_only fam_pl C0011K3 chr9:141127790:AG:A 1,.,. 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.204545,.,. -aff_only fam_pl C0011KA chr9:141127790:AG:A 1,.,1 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,45 0.146341,.,0.111111 -aff_only fam_pl IP00FNP chr9:141127790:AG:A 1,.,1 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,42 0.263158,.,0.238095 -aff_only fam_pl IP00FNW chr9:141127790:AG:A 1,.,. 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.266667,.,. -aff_only fam_pl IP00FNY chr9:141127790:AG:A 1,.,. 7 0.318 22 0.455 DB 533 28.3816 0 -1 7 0.318 55.53 -4.96 2.67 -1.09 0.694 -0.666 MQ -|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080||||| -1 0.138235 0.106121 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.285714,.,. -aff_only fam_pl C0011JZ chr10:38817730:G:A 1,.,. 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 222,.,. 0.157658,.,. -aff_only fam_pl C0011K2 chr10:38817730:G:A 1,.,. 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 214,.,. 0.186916,.,. -aff_only fam_pl C0011K3 chr10:38817730:G:A 1,.,. 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 561,.,. 0.0944742,.,. -aff_only fam_pl C0011KA chr10:38817730:G:A 1,.,1 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 189,.,214 0.248677,.,0.186916 -aff_only fam_pl IP00FNP chr10:38817730:G:A 1,.,1 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 589,.,222 0.14601,.,0.157658 -aff_only fam_pl IP00FNW chr10:38817730:G:A 1,.,. 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 404,.,. 0.232673,.,. -aff_only fam_pl IP00FNY chr10:38817730:G:A 1,.,. 7 0.318 22 -0.153 DB 4238 9.0714 0 -0.4667 7 0.318 53.89 0.051 3.46 -0.069 0.673 -2.741 MQ A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 424,.,. 0.200472,.,. -aff_only fam_pl C0011JZ chr10:47085032:CTT:C 1,.,. 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 0.9,.,. -aff_only fam_pl C0011K2 chr10:47085032:CTT:C 1,.,. 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,. 0.75,.,. -aff_only fam_pl C0011K3 chr10:47085032:CTT:C 1,.,. 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.791667,.,. -aff_only fam_pl C0011KA chr10:47085032:CTT:C 1,.,1 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,12 0.85,.,0.75 -aff_only fam_pl IP00FNP chr10:47085032:CTT:C 1,.,1 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,10 1,.,0.9 -aff_only fam_pl IP00FNW chr10:47085032:CTT:C 1,.,. 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,. 0.642857,.,. -aff_only fam_pl IP00FNY chr10:47085032:CTT:C 1,.,. 7 0.318 22 0 DB 842 3.0103 32.53 nan 7 0.318 60.1 0 23.04 0.246 0.644 3.51 MQRankSum -|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989||||| -1 0.175121 0.183934 3 3 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 8,.,. 1,.,. -aff_only fam_pl C0011JZ chr10:51484678:C:A 1,.,. 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.153846,.,. -aff_only fam_pl C0011K2 chr10:51484678:C:A 1,.,. 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.142857,.,. -aff_only fam_pl C0011K3 chr10:51484678:C:A 1,.,. 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.130435,.,. -aff_only fam_pl C0011KA chr10:51484678:C:A 1,.,1 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,49 0.136364,.,0.142857 -aff_only fam_pl IP00FNP chr10:51484678:C:A 1,.,1 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,39 0.25641,.,0.153846 -aff_only fam_pl IP00FNW chr10:51484678:C:A 1,.,. 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.181818,.,. -aff_only fam_pl IP00FNY chr10:51484678:C:A 1,.,. 7 0.318 22 0.757 407 9.0714 125.328 -0.4676 7 0.318 46.81 -1.797 4.38 -0.015 7.658 -140.8 SOR A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0755986 0.0770628 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.145833,.,. -aff_only fam_pl C0011JZ chr10:51484680:C:T 1,.,. 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.153846,.,. -aff_only fam_pl C0011K2 chr10:51484680:C:T 1,.,. 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.142857,.,. -aff_only fam_pl C0011K3 chr10:51484680:C:T 1,.,. 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.133333,.,. -aff_only fam_pl C0011KA chr10:51484680:C:T 1,.,1 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,49 0.136364,.,0.142857 -aff_only fam_pl IP00FNP chr10:51484680:C:T 1,.,1 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,39 0.25641,.,0.153846 -aff_only fam_pl IP00FNW chr10:51484680:C:T 1,.,. 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.212121,.,. -aff_only fam_pl IP00FNY chr10:51484680:C:T 1,.,. 7 0.318 22 1.26 406 9.0714 128.545 -0.4672 7 0.318 46.76 -1.739 4.41 0.194 7.701 -146.4 SOR T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.0797723 0.0813679 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.148936,.,. -aff_only fam_pl C0011JZ chr10:51484776:TTA:T 1,.,. 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.189189,.,. -aff_only fam_pl C0011K2 chr10:51484776:TTA:T 1,.,. 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.333333,.,. -aff_only fam_pl C0011K3 chr10:51484776:TTA:T 1,.,. 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.157895,.,. -aff_only fam_pl C0011KA chr10:51484776:TTA:T 1,.,1 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,42 0.208333,.,0.333333 -aff_only fam_pl IP00FNP chr10:51484776:TTA:T 1,.,1 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,37 0.217391,.,0.189189 -aff_only fam_pl IP00FNW chr10:51484776:TTA:T 1,.,. 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.142857,.,. -aff_only fam_pl IP00FNY chr10:51484776:TTA:T 1,.,. 7 0.318 22 0 DB 370 9.0714 52.172 -0.4667 7 0.318 35.31 -0.438 5.86 -0.742 3.021 6.76 FS -|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1||| -1 0.269477 0.274031 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.142857,.,. -aff_only fam_pl C0011JZ chr11:134629969:A:C 1,.,. 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.352941,.,. -aff_only fam_pl C0011K2 chr11:134629969:A:C 1,.,. 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.162791,.,. -aff_only fam_pl C0011K3 chr11:134629969:A:C 1,.,. 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.152174,.,. -aff_only fam_pl C0011KA chr11:134629969:A:C 1,.,1 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,43 0.25,.,0.162791 -aff_only fam_pl IP00FNP chr11:134629969:A:C 1,.,1 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,34 0.180328,.,0.352941 -aff_only fam_pl IP00FNW chr11:134629969:A:C 1,.,. 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 83,.,. 0.493976,.,. -aff_only fam_pl IP00FNY chr11:134629969:A:C 1,.,. 7 0.318 22 -0.254 DB 587 9.0714 38.555 -0.5714 8 0.364 50.54 0.22 10.67 -1.48 1.328 -12.21 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.389133 0.396508 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 97,.,. 0.515464,.,. -aff_only fam_pl C0011JZ chr11:134629972:A:C 1,.,. 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.342857,.,. -aff_only fam_pl C0011K2 chr11:134629972:A:C 1,.,. 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.162791,.,. -aff_only fam_pl C0011K3 chr11:134629972:A:C 1,.,. 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.139535,.,. -aff_only fam_pl C0011KA chr11:134629972:A:C 1,.,1 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,43 0.25,.,0.162791 -aff_only fam_pl IP00FNP chr11:134629972:A:C 1,.,1 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,35 0.135593,.,0.342857 -aff_only fam_pl IP00FNW chr11:134629972:A:C 1,.,. 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 79,.,. 0.493671,.,. -aff_only fam_pl IP00FNY chr11:134629972:A:C 1,.,. 7 0.318 22 -0.511 DB 570 11.8014 24.473 -0.6923 8 0.364 50.58 0.169 10.09 -0.579 1.466 -5.583 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.411614 0.424807 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 96,.,. 0.479167,.,. -aff_only fam_pl C0011JZ chr12:334342:C:T 1,.,. 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.702703,.,. -aff_only fam_pl C0011K2 chr12:334342:C:T 1,.,. 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.480769,.,. -aff_only fam_pl C0011K3 chr12:334342:C:T 1,.,. 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.604651,.,. -aff_only fam_pl C0011KA chr12:334342:C:T 1,.,1 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,52 0.414634,.,0.480769 -aff_only fam_pl IP00FNP chr12:334342:C:T 1,.,1 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,37 0.480769,.,0.702703 -aff_only fam_pl IP00FNW chr12:334342:C:T 1,.,. 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.390244,.,. -aff_only fam_pl IP00FNY chr12:334342:C:T 1,.,. 7 0.318 22 -1.139 DB 491 9.0714 1.344 -0.4667 7 0.318 60 0 14.58 0.099 0.597 23.72 MQRankSum T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046||||| -1 0.301969 0.283645 986 555 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.59322,.,. -aff_only fam_pl C0011JZ chr12:2033347:C:T 1,.,. 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.314286,.,. -aff_only fam_pl C0011K2 chr12:2033347:C:T 1,.,. 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.489362,.,. -aff_only fam_pl C0011K3 chr12:2033347:C:T 1,.,. 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.536585,.,. -aff_only fam_pl C0011KA chr12:2033347:C:T 1,.,1 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,47 0.583333,.,0.489362 -aff_only fam_pl IP00FNP chr12:2033347:C:T 1,.,1 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,35 0.35,.,0.314286 -aff_only fam_pl IP00FNW chr12:2033347:C:T 1,.,. 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr12:2033347:C:T 1,.,. 7 0.318 22 2.3 DB 447 9.0714 3.976 -0.4667 7 0.318 51.96 -2.758 13.16 0.482 0.918 -2.23 MQ T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES|||| -1 0.481677 0.556349 2670 2075 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.576923,.,. -aff_only fam_pl C0011JZ chr12:2036141:T:C 1,.,. 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.514286,.,. -aff_only fam_pl C0011K2 chr12:2036141:T:C 1,.,. 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.535714,.,. -aff_only fam_pl C0011K3 chr12:2036141:T:C 1,.,. 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.325,.,. -aff_only fam_pl C0011KA chr12:2036141:T:C 1,.,1 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,56 0.416667,.,0.535714 -aff_only fam_pl IP00FNP chr12:2036141:T:C 1,.,1 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,35 0.52,.,0.514286 -aff_only fam_pl IP00FNW chr12:2036141:T:C 1,.,. 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.45,.,. -aff_only fam_pl IP00FNY chr12:2036141:T:C 1,.,. 7 0.318 22 -2.006 DB 477 9.0714 24.678 -0.4667 7 0.318 60 0 12.12 0.49 0.465 16.93 MQRankSum C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES|||| -1 0.469936 0.558798 2687 2135 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 64,.,. 0.515625,.,. -aff_only fam_pl C0011JZ chr12:5569271:C:T 1,.,. 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.558824,.,. -aff_only fam_pl C0011K2 chr12:5569271:C:T 1,.,. 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.479167,.,. -aff_only fam_pl C0011K3 chr12:5569271:C:T 1,.,. 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.625,.,. -aff_only fam_pl C0011KA chr12:5569271:C:T 1,.,1 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,48 0.347826,.,0.479167 -aff_only fam_pl IP00FNP chr12:5569271:C:T 1,.,1 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,34 0.5,.,0.558824 -aff_only fam_pl IP00FNW chr12:5569271:C:T 1,.,. 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr12:5569271:C:T 1,.,. 7 0.318 22 0 DB 466 9.0714 16.139 -0.4667 7 0.318 60 0 14.34 -0.783 0.967 21.94 MQRankSum T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023||||| -1 0.617836 0.555637 4097 2064 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 68,.,. 0.544118,.,. -aff_only fam_pl C0011JZ chr12:6744864:G:C 1,.,. 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.291667,.,. -aff_only fam_pl C0011K2 chr12:6744864:G:C 1,.,. 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.586957,.,. -aff_only fam_pl C0011K3 chr12:6744864:G:C 1,.,. 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.425532,.,. -aff_only fam_pl C0011KA chr12:6744864:G:C 1,.,1 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,46 0.594595,.,0.586957 -aff_only fam_pl IP00FNP chr12:6744864:G:C 1,.,1 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,24 0.42,.,0.291667 -aff_only fam_pl IP00FNW chr12:6744864:G:C 1,.,. 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.34375,.,. -aff_only fam_pl IP00FNY chr12:6744864:G:C 1,.,. 7 0.318 22 -0.314 DB 446 9.0714 10.015 -0.4667 7 0.318 60 0 11.9 -0.191 0.373 23.73 MQRankSum C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195||||| -1 0.536383 0.568792 3155 2202 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 67,.,. 0.41791,.,. -aff_only fam_pl C0011JZ chr12:8335722:A:T 1,.,. 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.296296,.,. -aff_only fam_pl C0011K2 chr12:8335722:A:T 1,.,. 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,. 0.565217,.,. -aff_only fam_pl C0011K3 chr12:8335722:A:T 1,.,. 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.363636,.,. -aff_only fam_pl C0011KA chr12:8335722:A:T 1,.,1 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,23 0.538462,.,0.565217 -aff_only fam_pl IP00FNP chr12:8335722:A:T 1,.,1 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,27 0.351351,.,0.296296 -aff_only fam_pl IP00FNW chr12:8335722:A:T 1,.,. 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.458333,.,. -aff_only fam_pl IP00FNY chr12:8335722:A:T 1,.,. 7 0.318 22 -0.355 DB 476 9.0714 3.734 -0.4667 7 0.318 60.49 0 16.37 0.309 0.966 3.93 MQRankSum T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES|||| -1 0.138584 0.128167 193 100 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.42,.,. -aff_only fam_pl C0011JZ chr12:9739997:C:A 1,.,. 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.444444,.,. -aff_only fam_pl C0011K2 chr12:9739997:C:A 1,.,. 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.510638,.,. -aff_only fam_pl C0011K3 chr12:9739997:C:A 1,.,. 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.46875,.,. -aff_only fam_pl C0011KA chr12:9739997:C:A 1,.,1 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,47 0.5625,.,0.510638 -aff_only fam_pl IP00FNP chr12:9739997:C:A 1,.,1 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,36 0.489796,.,0.444444 -aff_only fam_pl IP00FNW chr12:9739997:C:A 1,.,. 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.472222,.,. -aff_only fam_pl IP00FNY chr12:9739997:C:A 1,.,. 7 0.318 22 0.066 DB 433 9.0714 0.418 -0.4667 7 0.318 60 0 13.93 0.399 0.665 23.76 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.466522 0.493146 2305 1620 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,. 0.560606,.,. -aff_only fam_pl C0011JZ chr12:9740839:G:A 1,.,. 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.441176,.,. -aff_only fam_pl C0011K2 chr12:9740839:G:A 1,.,. 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.590909,.,. -aff_only fam_pl C0011K3 chr12:9740839:G:A 1,.,. 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.463415,.,. -aff_only fam_pl C0011KA chr12:9740839:G:A 1,.,1 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,44 0.648649,.,0.590909 -aff_only fam_pl IP00FNP chr12:9740839:G:A 1,.,1 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,34 0.513514,.,0.441176 -aff_only fam_pl IP00FNW chr12:9740839:G:A 1,.,. 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.390244,.,. -aff_only fam_pl IP00FNY chr12:9740839:G:A 1,.,. 7 0.318 22 0.978 DB 463 9.0714 0 -0.4667 7 0.318 60 0 15.14 -0.321 0.68 23.84 MQRankSum A|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.395541 0.452966 1773 1356 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,. 0.589041,.,. -aff_only fam_pl C0011JZ chr12:9745571:A:G 1,.,. 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.689655,.,. -aff_only fam_pl C0011K2 chr12:9745571:A:G 1,.,. 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.604651,.,. -aff_only fam_pl C0011K3 chr12:9745571:A:G 1,.,. 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.466667,.,. -aff_only fam_pl C0011KA chr12:9745571:A:G 1,.,1 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,43 0.517241,.,0.604651 -aff_only fam_pl IP00FNP chr12:9745571:A:G 1,.,1 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,29 0.424242,.,0.689655 -aff_only fam_pl IP00FNW chr12:9745571:A:G 1,.,. 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.446429,.,. -aff_only fam_pl IP00FNY chr12:9745571:A:G 1,.,. 7 0.318 22 -0.912 DB 489 9.0714 10.836 -0.4667 7 0.318 60 0 11.87 -0.08 1.147 23.83 MQRankSum G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446882 0.493154 2176 1624 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 74,.,. 0.445946,.,. -aff_only fam_pl C0011JZ chr12:9746600:T:C 1,.,. 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr12:9746600:T:C 1,.,. 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.529412,.,. -aff_only fam_pl C0011K3 chr12:9746600:T:C 1,.,. 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.555556,.,. -aff_only fam_pl C0011KA chr12:9746600:T:C 1,.,1 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,51 0.5,.,0.529412 -aff_only fam_pl IP00FNP chr12:9746600:T:C 1,.,1 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 67,.,40 0.537313,.,0.5 -aff_only fam_pl IP00FNW chr12:9746600:T:C 1,.,. 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.52381,.,. -aff_only fam_pl IP00FNY chr12:9746600:T:C 1,.,. 7 0.318 22 0.035 DB 495 9.0714 0 -0.4667 7 0.318 60 0 14.96 0.73 0.682 23.48 MQRankSum C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.446344 0.493239 2177 1629 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.521739,.,. -aff_only fam_pl C0011JZ chr12:9747513:G:A 1,.,. 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 8,.,. 1,.,. -aff_only fam_pl C0011K2 chr12:9747513:G:A 1,.,. 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 1,.,. -aff_only fam_pl C0011K3 chr12:9747513:G:A 1,.,. 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 1,.,. -aff_only fam_pl C0011KA chr12:9747513:G:A 1,.,1 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 12,.,17 1,.,1 -aff_only fam_pl IP00FNP chr12:9747513:G:A 1,.,1 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,8 1,.,1 -aff_only fam_pl IP00FNW chr12:9747513:G:A 1,.,. 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 1,.,. -aff_only fam_pl IP00FNY chr12:9747513:G:A 1,.,. 7 0.318 22 . DB 454 3.0103 0 nan 7 0.318 60.05 . 30.83 . 0.831 3.44 QD A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.586462 0.570162 3709 2184 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 1,.,. -aff_only fam_pl C0011JZ chr12:9747557:T:A 1,.,. 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.4,.,. -aff_only fam_pl C0011K2 chr12:9747557:T:A 1,.,. 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.432432,.,. -aff_only fam_pl C0011K3 chr12:9747557:T:A 1,.,. 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.44186,.,. -aff_only fam_pl C0011KA chr12:9747557:T:A 1,.,1 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,37 0.461538,.,0.432432 -aff_only fam_pl IP00FNP chr12:9747557:T:A 1,.,1 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,20 0.62,.,0.4 -aff_only fam_pl IP00FNW chr12:9747557:T:A 1,.,. 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.463415,.,. -aff_only fam_pl IP00FNY chr12:9747557:T:A 1,.,. 7 0.318 22 0.22 DB 435 9.0714 6.421 -0.4667 7 0.318 60 0 13.99 0.122 1.035 24.26 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.471313 0.492262 2348 1613 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 60,.,. 0.583333,.,. -aff_only fam_pl C0011JZ chr12:9747676:G:A 1,.,. 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.30303,.,. -aff_only fam_pl C0011K2 chr12:9747676:G:A 1,.,. 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.351351,.,. -aff_only fam_pl C0011K3 chr12:9747676:G:A 1,.,. 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.555556,.,. -aff_only fam_pl C0011KA chr12:9747676:G:A 1,.,1 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,37 0.545455,.,0.351351 -aff_only fam_pl IP00FNP chr12:9747676:G:A 1,.,1 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,33 0.719298,.,0.30303 -aff_only fam_pl IP00FNW chr12:9747676:G:A 1,.,. 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.471698,.,. -aff_only fam_pl IP00FNY chr12:9747676:G:A 1,.,. 7 0.318 22 -0.615 DB 483 9.0714 8.229 -0.4667 7 0.318 60 0 14.15 0.796 0.422 23.96 MQRankSum A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.474057 0.495801 2374 1634 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.485714,.,. -aff_only fam_pl C0011JZ chr12:9748572:T:C 1,.,. 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.731707,.,. -aff_only fam_pl C0011K2 chr12:9748572:T:C 1,.,. 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.354839,.,. -aff_only fam_pl C0011K3 chr12:9748572:T:C 1,.,. 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.403846,.,. -aff_only fam_pl C0011KA chr12:9748572:T:C 1,.,1 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,31 0.545455,.,0.354839 -aff_only fam_pl IP00FNP chr12:9748572:T:C 1,.,1 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,41 0.571429,.,0.731707 -aff_only fam_pl IP00FNW chr12:9748572:T:C 1,.,. 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.553191,.,. -aff_only fam_pl IP00FNY chr12:9748572:T:C 1,.,. 7 0.318 22 0.149 DB 488 9.0714 19.998 -0.4667 7 0.318 60 0 15.11 -0.324 0.71 20.5 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490104 0.497058 2536 1645 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 77,.,. 0.545455,.,. -aff_only fam_pl C0011JZ chr12:9749543:G:A 1,.,. 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.461538,.,. -aff_only fam_pl C0011K2 chr12:9749543:G:A 1,.,. 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.611111,.,. -aff_only fam_pl C0011K3 chr12:9749543:G:A 1,.,. 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.411765,.,. -aff_only fam_pl C0011KA chr12:9749543:G:A 1,.,1 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,54 0.52381,.,0.611111 -aff_only fam_pl IP00FNP chr12:9749543:G:A 1,.,1 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,39 0.412698,.,0.461538 -aff_only fam_pl IP00FNW chr12:9749543:G:A 1,.,. 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.508475,.,. -aff_only fam_pl IP00FNY chr12:9749543:G:A 1,.,. 7 0.318 22 -0.812 DB 526 9.0714 3.932 -0.4667 7 0.318 60 0 13.3 -0.296 0.879 23.49 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.321233 0.362097 1192 872 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 78,.,. 0.448718,.,. -aff_only fam_pl C0011JZ chr12:9749682:T:C 1,.,. 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.555556,.,. -aff_only fam_pl C0011K2 chr12:9749682:T:C 1,.,. 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.6,.,. -aff_only fam_pl C0011K3 chr12:9749682:T:C 1,.,. 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.606061,.,. -aff_only fam_pl C0011KA chr12:9749682:T:C 1,.,1 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,45 0.666667,.,0.6 -aff_only fam_pl IP00FNP chr12:9749682:T:C 1,.,1 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 68,.,36 0.5,.,0.555556 -aff_only fam_pl IP00FNW chr12:9749682:T:C 1,.,. 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,. 0.527273,.,. -aff_only fam_pl IP00FNY chr12:9749682:T:C 1,.,. 7 0.318 22 -0.239 DB 496 9.0714 2.311 -0.4667 7 0.318 60 0 15.49 -0.203 0.828 23.45 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.4901 0.496908 2537 1643 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 76,.,. 0.513158,.,. -aff_only fam_pl C0011JZ chr12:9749726:G:T 1,.,. 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.482759,.,. -aff_only fam_pl C0011K2 chr12:9749726:G:T 1,.,. 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.531915,.,. -aff_only fam_pl C0011K3 chr12:9749726:G:T 1,.,. 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.558824,.,. -aff_only fam_pl C0011KA chr12:9749726:G:T 1,.,1 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,47 0.636364,.,0.531915 -aff_only fam_pl IP00FNP chr12:9749726:G:T 1,.,1 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,29 0.424242,.,0.482759 -aff_only fam_pl IP00FNW chr12:9749726:G:T 1,.,. 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.542373,.,. -aff_only fam_pl IP00FNY chr12:9749726:G:T 1,.,. 7 0.318 22 0.299 DB 498 9.0714 0.385 -0.4667 7 0.318 60 0 14.13 -0.021 0.67 23.47 MQRankSum T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.490522 0.497572 2538 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.4625,.,. -aff_only fam_pl C0011JZ chr12:9752576:TAA:T 1,.,. 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 1,.,. -aff_only fam_pl C0011K2 chr12:9752576:TAA:T 1,.,. 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 1,.,. -aff_only fam_pl C0011K3 chr12:9752576:TAA:T 1,.,. 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 1,.,. -aff_only fam_pl C0011KA chr12:9752576:TAA:T 1,.,1 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,10 0.944444,.,1 -aff_only fam_pl IP00FNP chr12:9752576:TAA:T 1,.,1 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,10 1,.,1 -aff_only fam_pl IP00FNW chr12:9752576:TAA:T 1,.,. 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 1,.,. -aff_only fam_pl IP00FNY chr12:9752576:TAA:T 1,.,. 7 0.318 22 1.64 DB 435 3.0103 0 nan 7 0.318 60.07 0.371 33.56 1.73 1.108 -0.6292 MQRankSum -|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.468831 0.507347 1899 1416 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 1,.,. -aff_only fam_pl C0011JZ chr12:9755905:G:A 1,.,. 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.682927,.,. -aff_only fam_pl C0011K2 chr12:9755905:G:A 1,.,. 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.591837,.,. -aff_only fam_pl C0011K3 chr12:9755905:G:A 1,.,. 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.644444,.,. -aff_only fam_pl C0011KA chr12:9755905:G:A 1,.,1 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,49 0.53125,.,0.591837 -aff_only fam_pl IP00FNP chr12:9755905:G:A 1,.,1 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,41 0.5,.,0.682927 -aff_only fam_pl IP00FNW chr12:9755905:G:A 1,.,. 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr12:9755905:G:A 1,.,. 7 0.318 22 -0.411 DB 474 9.0714 11.705 -0.4667 7 0.318 60.03 0 15.49 -0.815 1.213 7.16 MQRankSum A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.371155 0.369347 1482 897 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,. 0.454545,.,. -aff_only fam_pl C0011JZ chr12:9756021:C:CTATT 1,.,. 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.607143,.,. -aff_only fam_pl C0011K2 chr12:9756021:C:CTATT 1,.,. 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.514286,.,. -aff_only fam_pl C0011K3 chr12:9756021:C:CTATT 1,.,. 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.551724,.,. -aff_only fam_pl C0011KA chr12:9756021:C:CTATT 1,.,1 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,35 0.538462,.,0.514286 -aff_only fam_pl IP00FNP chr12:9756021:C:CTATT 1,.,1 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,28 0.414634,.,0.607143 -aff_only fam_pl IP00FNW chr12:9756021:C:CTATT 1,.,. 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.571429,.,. -aff_only fam_pl IP00FNY chr12:9756021:C:CTATT 1,.,. 7 0.318 22 0 DB 463 9.0714 2.879 -0.4667 7 0.318 60.03 0 20.84 -0.093 0.847 10.46 MQRankSum TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.358611 0.357388 1344 823 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.585366,.,. -aff_only fam_pl C0011JZ chr12:9759244:T:TTA 1,.,. 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.444444,.,. -aff_only fam_pl C0011K2 chr12:9759244:T:TTA 1,.,. 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,. 0.434783,.,. -aff_only fam_pl C0011K3 chr12:9759244:T:TTA 1,.,. 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.40625,.,. -aff_only fam_pl C0011KA chr12:9759244:T:TTA 1,.,1 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,23 0.5,.,0.434783 -aff_only fam_pl IP00FNP chr12:9759244:T:TTA 1,.,1 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,18 0.6,.,0.444444 -aff_only fam_pl IP00FNW chr12:9759244:T:TTA 1,.,. 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,. 0.631579,.,. -aff_only fam_pl IP00FNY chr12:9759244:T:TTA 1,.,. 7 0.318 22 0.412 DB 333 9.0714 16.613 -0.4667 7 0.318 59.48 0 14.14 -0.403 0.218 4.79 MQRankSum TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.460276 0.480533 1430 1075 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.404762,.,. -aff_only fam_pl C0011JZ chr12:9759465:A:C 1,.,. 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.590909,.,. -aff_only fam_pl C0011K2 chr12:9759465:A:C 1,.,. 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr12:9759465:A:C 1,.,. 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.325581,.,. -aff_only fam_pl C0011KA chr12:9759465:A:C 1,.,1 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,38 0.555556,.,0.5 -aff_only fam_pl IP00FNP chr12:9759465:A:C 1,.,1 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,22 0.472222,.,0.590909 -aff_only fam_pl IP00FNW chr12:9759465:A:C 1,.,. 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.421053,.,. -aff_only fam_pl IP00FNY chr12:9759465:A:C 1,.,. 7 0.318 22 0.207 DB 411 9.0714 3.51 -0.4667 7 0.318 60 0 12.52 -0.122 0.517 23.24 MQRankSum C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378239 0.421036 1567 1108 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.474576,.,. -aff_only fam_pl C0011JZ chr12:9761465:C:G 1,.,. 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.388889,.,. -aff_only fam_pl C0011K2 chr12:9761465:C:G 1,.,. 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.227273,.,. -aff_only fam_pl C0011K3 chr12:9761465:C:G 1,.,. 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.47619,.,. -aff_only fam_pl C0011KA chr12:9761465:C:G 1,.,1 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,22 0.46875,.,0.227273 -aff_only fam_pl IP00FNP chr12:9761465:C:G 1,.,1 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,36 0.444444,.,0.388889 -aff_only fam_pl IP00FNW chr12:9761465:C:G 1,.,. 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.410256,.,. -aff_only fam_pl IP00FNY chr12:9761465:C:G 1,.,. 7 0.318 22 0.651 DB 393 9.0714 0.939 -0.4667 7 0.318 52.36 -1.34 12.23 0.243 0.732 -2.365 MQ G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.380015 0.423276 1658 1180 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.589744,.,. -aff_only fam_pl C0011JZ chr12:9763589:C:T 1,.,. 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.53125,.,. -aff_only fam_pl C0011K2 chr12:9763589:C:T 1,.,. 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.622222,.,. -aff_only fam_pl C0011K3 chr12:9763589:C:T 1,.,. 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.487805,.,. -aff_only fam_pl C0011KA chr12:9763589:C:T 1,.,1 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,45 0.45,.,0.622222 -aff_only fam_pl IP00FNP chr12:9763589:C:T 1,.,1 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,32 0.517857,.,0.53125 -aff_only fam_pl IP00FNW chr12:9763589:C:T 1,.,. 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.461538,.,. -aff_only fam_pl IP00FNY chr12:9763589:C:T 1,.,. 7 0.318 22 1.07 DB 489 9.0714 0 -0.4667 7 0.318 59.98 0 14.01 -0.276 0.678 7.72 MQRankSum T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.37913 0.422091 1660 1181 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 71,.,. 0.478873,.,. -aff_only fam_pl C0011JZ chr12:9763737:G:A 1,.,. 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.666667,.,. -aff_only fam_pl C0011K2 chr12:9763737:G:A 1,.,. 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.55,.,. -aff_only fam_pl C0011K3 chr12:9763737:G:A 1,.,. 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.538462,.,. -aff_only fam_pl C0011KA chr12:9763737:G:A 1,.,1 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,40 0.787879,.,0.55 -aff_only fam_pl IP00FNP chr12:9763737:G:A 1,.,1 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,33 0.463415,.,0.666667 -aff_only fam_pl IP00FNW chr12:9763737:G:A 1,.,. 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.634146,.,. -aff_only fam_pl IP00FNY chr12:9763737:G:A 1,.,. 7 0.318 22 0.508 DB 448 9.0714 7 -0.4667 7 0.318 59.78 0 16.81 0.294 0.79 6.83 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.378565 0.421863 1653 1176 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.564516,.,. -aff_only fam_pl C0011JZ chr12:9764897:G:A 1,.,. 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr12:9764897:G:A 1,.,. 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.454545,.,. -aff_only fam_pl C0011K3 chr12:9764897:G:A 1,.,. 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.536585,.,. -aff_only fam_pl C0011KA chr12:9764897:G:A 1,.,1 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,44 0.444444,.,0.454545 -aff_only fam_pl IP00FNP chr12:9764897:G:A 1,.,1 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,26 0.479167,.,0.5 -aff_only fam_pl IP00FNW chr12:9764897:G:A 1,.,. 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.511628,.,. -aff_only fam_pl IP00FNY chr12:9764897:G:A 1,.,. 7 0.318 22 -0.64 DB 450 9.0714 0.867 -0.4667 7 0.318 58.53 0 13.7 -0.967 0.626 4.92 MQRankSum A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1||| -1 0.379082 0.422317 1658 1178 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.57971,.,. -aff_only fam_pl C0011JZ chr12:9769429:CAGAG:C 1,.,. 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,. 0.526316,.,. -aff_only fam_pl C0011K2 chr12:9769429:CAGAG:C 1,.,. 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 15,.,. 0.4,.,. -aff_only fam_pl C0011K3 chr12:9769429:CAGAG:C 1,.,. 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.388889,.,. -aff_only fam_pl C0011KA chr12:9769429:CAGAG:C 1,.,1 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,15 0.444444,.,0.4 -aff_only fam_pl IP00FNP chr12:9769429:CAGAG:C 1,.,1 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,19 0.375,.,0.526316 -aff_only fam_pl IP00FNW chr12:9769429:CAGAG:C 1,.,. 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.352941,.,. -aff_only fam_pl IP00FNY chr12:9769429:CAGAG:C 1,.,. 7 0.318 22 0.878 DB 341 9.0714 0.621 -0.5455 8 0.364 59.59 0 15.12 -0.082 0.781 6.29 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.379867 0.42454 1287 922 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.392857,.,. -aff_only fam_pl C0011JZ chr12:9779878:T:A 1,.,. 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.555556,.,. -aff_only fam_pl C0011K2 chr12:9779878:T:A 1,.,. 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.581395,.,. -aff_only fam_pl C0011K3 chr12:9779878:T:A 1,.,. 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.547619,.,. -aff_only fam_pl C0011KA chr12:9779878:T:A 1,.,1 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,43 0.441176,.,0.581395 -aff_only fam_pl IP00FNP chr12:9779878:T:A 1,.,1 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,18 0.489796,.,0.555556 -aff_only fam_pl IP00FNW chr12:9779878:T:A 1,.,. 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.614035,.,. -aff_only fam_pl IP00FNY chr12:9779878:T:A 1,.,. 7 0.318 22 1.15 DB 448 9.0714 5.097 -0.4667 7 0.318 59.98 0 21.29 0.493 0.473 7.39 MQRankSum A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES|||| -1 0.377381 0.419781 1544 1098 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 75,.,. 0.586667,.,. -aff_only fam_pl C0011JZ chr12:9780206:C:T 1,.,. 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.545455,.,. -aff_only fam_pl C0011K2 chr12:9780206:C:T 1,.,. 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.477273,.,. -aff_only fam_pl C0011K3 chr12:9780206:C:T 1,.,. 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.491525,.,. -aff_only fam_pl C0011KA chr12:9780206:C:T 1,.,1 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,44 0.592593,.,0.477273 -aff_only fam_pl IP00FNP chr12:9780206:C:T 1,.,1 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 60,.,33 0.583333,.,0.545455 -aff_only fam_pl IP00FNW chr12:9780206:C:T 1,.,. 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.553191,.,. -aff_only fam_pl IP00FNY chr12:9780206:C:T 1,.,. 7 0.318 22 0 DB 463 9.0714 1.317 -0.4667 7 0.318 56.16 0 14.86 -0.038 0.615 -0.0261 MQ T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES|||| -1 0.379998 0.422834 1668 1190 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.461538,.,. -aff_only fam_pl C0011JZ chr12:9780577:A:G 1,.,. 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.475,.,. -aff_only fam_pl C0011K2 chr12:9780577:A:G 1,.,. 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.542857,.,. -aff_only fam_pl C0011K3 chr12:9780577:A:G 1,.,. 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.547619,.,. -aff_only fam_pl C0011KA chr12:9780577:A:G 1,.,1 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,35 0.366667,.,0.542857 -aff_only fam_pl IP00FNP chr12:9780577:A:G 1,.,1 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,40 0.454545,.,0.475 -aff_only fam_pl IP00FNW chr12:9780577:A:G 1,.,. 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.488372,.,. -aff_only fam_pl IP00FNY chr12:9780577:A:G 1,.,. 7 0.318 22 -1.863 DB 433 9.0714 10.22 -0.4667 7 0.318 53.72 -1.397 11.78 -0.118 0.395 -1.207 MQ G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES|||| -1 0.379642 0.422698 1670 1189 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.392157,.,. -aff_only fam_pl C0011JZ chr12:9780843:T:C 1,.,. 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.393939,.,. -aff_only fam_pl C0011K2 chr12:9780843:T:C 1,.,. 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.390244,.,. -aff_only fam_pl C0011K3 chr12:9780843:T:C 1,.,. 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.65625,.,. -aff_only fam_pl C0011KA chr12:9780843:T:C 1,.,1 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,41 0.527778,.,0.390244 -aff_only fam_pl IP00FNP chr12:9780843:T:C 1,.,1 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,33 0.4375,.,0.393939 -aff_only fam_pl IP00FNW chr12:9780843:T:C 1,.,. 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.473684,.,. -aff_only fam_pl IP00FNY chr12:9780843:T:C 1,.,. 7 0.318 22 -0.793 DB 448 9.0714 13.633 -0.4667 7 0.318 49.22 -0.287 12.96 0.147 0.321 -2.572 MQ C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES|||| 11 0.378809 0.421603 1655 1174 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 60,.,. 0.516667,.,. -aff_only fam_pl C0011JZ chr12:9997789:A:T 1,.,. 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr12:9997789:A:T 1,.,. 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.55814,.,. -aff_only fam_pl C0011K3 chr12:9997789:A:T 1,.,. 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.405405,.,. -aff_only fam_pl C0011KA chr12:9997789:A:T 1,.,1 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,43 0.588235,.,0.55814 -aff_only fam_pl IP00FNP chr12:9997789:A:T 1,.,1 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 67,.,36 0.477612,.,0.5 -aff_only fam_pl IP00FNW chr12:9997789:A:T 1,.,. 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,. 0.490909,.,. -aff_only fam_pl IP00FNY chr12:9997789:A:T 1,.,. 7 0.318 22 0 DB 472 9.0714 0 -0.4667 7 0.318 59.39 0 14.13 -0.367 0.71 6.27 MQRankSum T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342||||| -1 0.243354 0.298999 721 601 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 59,.,. 0.474576,.,. -aff_only fam_pl C0011JZ chr12:10003185:C:T 1,.,. 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.567568,.,. -aff_only fam_pl C0011K2 chr12:10003185:C:T 1,.,. 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr12:10003185:C:T 1,.,. 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.451613,.,. -aff_only fam_pl C0011KA chr12:10003185:C:T 1,.,1 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,40 0.529412,.,0.5 -aff_only fam_pl IP00FNP chr12:10003185:C:T 1,.,1 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,37 0.5,.,0.567568 -aff_only fam_pl IP00FNW chr12:10003185:C:T 1,.,. 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.515152,.,. -aff_only fam_pl IP00FNY chr12:10003185:C:T 1,.,. 7 0.318 22 1.05 DB 470 9.0714 9.244 -0.4667 7 0.318 60.03 0 14.36 -0.293 1.101 7.49 MQRankSum T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053||||| -1 0.0481495 0.0645566 30 26 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 83,.,. 0.506024,.,. -aff_only fam_pl C0011JZ chr12:10177037:G:A 1,.,. 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.511628,.,. -aff_only fam_pl C0011K2 chr12:10177037:G:A 1,.,. 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr12:10177037:G:A 1,.,. 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.538462,.,. -aff_only fam_pl C0011KA chr12:10177037:G:A 1,.,1 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,46 0.464286,.,0.5 -aff_only fam_pl IP00FNP chr12:10177037:G:A 1,.,1 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,43 0.454545,.,0.511628 -aff_only fam_pl IP00FNW chr12:10177037:G:A 1,.,. 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 67,.,. 0.522388,.,. -aff_only fam_pl IP00FNY chr12:10177037:G:A 1,.,. 7 0.318 22 0 DB 503 9.0714 1.729 -0.4667 7 0.318 60 0 14.78 -0.345 0.772 23.72 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.304713 0.348498 1069 821 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,. 0.606061,.,. -aff_only fam_pl C0011JZ chr16:80636220:A:T 1,.,. 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.606061,.,. -aff_only fam_pl C0011K2 chr16:80636220:A:T 1,.,. 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.534884,.,. -aff_only fam_pl C0011K3 chr16:80636220:A:T 1,.,. 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.806452,.,. -aff_only fam_pl C0011KA chr16:80636220:A:T 1,.,1 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,43 0.452381,.,0.534884 -aff_only fam_pl IP00FNP chr16:80636220:A:T 1,.,1 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,33 0.507692,.,0.606061 -aff_only fam_pl IP00FNW chr16:80636220:A:T 1,.,. 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.477273,.,. -aff_only fam_pl IP00FNY chr16:80636220:A:T 1,.,. 7 0.318 22 -0.408 DB 457 9.0714 2.414 -0.4667 7 0.318 59.96 0 15.37 0.505 0.831 8.64 MQRankSum T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.180142 0.166176 396 214 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 58,.,. 0.517241,.,. -aff_only fam_pl C0011JZ chr16:80636297:C:G 1,.,. 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.642857,.,. -aff_only fam_pl C0011K2 chr16:80636297:C:G 1,.,. 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.641026,.,. -aff_only fam_pl C0011K3 chr16:80636297:C:G 1,.,. 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.611111,.,. -aff_only fam_pl C0011KA chr16:80636297:C:G 1,.,1 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,39 0.5,.,0.641026 -aff_only fam_pl IP00FNP chr16:80636297:C:G 1,.,1 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,28 0.377358,.,0.642857 -aff_only fam_pl IP00FNW chr16:80636297:C:G 1,.,. 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.4,.,. -aff_only fam_pl IP00FNY chr16:80636297:C:G 1,.,. 7 0.318 22 1.31 DB 457 9.0714 4.295 -0.4667 7 0.318 59.96 0 13.62 -0.406 0.84 8.59 MQRankSum G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.219375 0.169686 618 219 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.442857,.,. -aff_only fam_pl C0011JZ chr16:80636940:G:A 1,.,. 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.580645,.,. -aff_only fam_pl C0011K2 chr16:80636940:G:A 1,.,. 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.576923,.,. -aff_only fam_pl C0011K3 chr16:80636940:G:A 1,.,. 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.5,.,. -aff_only fam_pl C0011KA chr16:80636940:G:A 1,.,1 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,52 0.72973,.,0.576923 -aff_only fam_pl IP00FNP chr16:80636940:G:A 1,.,1 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 68,.,31 0.529412,.,0.580645 -aff_only fam_pl IP00FNW chr16:80636940:G:A 1,.,. 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.395833,.,. -aff_only fam_pl IP00FNY chr16:80636940:G:A 1,.,. 7 0.318 22 0.786 DB 495 9.0714 0.388 -0.4667 7 0.318 60.16 0 15.67 0.582 0.668 7.82 MQRankSum A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.170014 0.156388 356 187 36 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.57377,.,. -aff_only fam_pl C0011JZ chr16:80639833:T:G 1,.,. 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.529412,.,. -aff_only fam_pl C0011K2 chr16:80639833:T:G 1,.,. 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.46,.,. -aff_only fam_pl C0011K3 chr16:80639833:T:G 1,.,. 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.5,.,. -aff_only fam_pl C0011KA chr16:80639833:T:G 1,.,1 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,50 0.511111,.,0.46 -aff_only fam_pl IP00FNP chr16:80639833:T:G 1,.,1 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,34 0.5,.,0.529412 -aff_only fam_pl IP00FNW chr16:80639833:T:G 1,.,. 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.681818,.,. -aff_only fam_pl IP00FNY chr16:80639833:T:G 1,.,. 7 0.318 22 0.055 DB 482 9.0714 0.399 -0.4667 7 0.318 60 0 20.66 0.352 0.704 22.13 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222752 0.17895 592 223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.5,.,. -aff_only fam_pl C0011JZ chr16:80639836:G:A 1,.,. 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.529412,.,. -aff_only fam_pl C0011K2 chr16:80639836:G:A 1,.,. 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.46,.,. -aff_only fam_pl C0011K3 chr16:80639836:G:A 1,.,. 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.5,.,. -aff_only fam_pl C0011KA chr16:80639836:G:A 1,.,1 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,50 0.533333,.,0.46 -aff_only fam_pl IP00FNP chr16:80639836:G:A 1,.,1 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,34 0.491803,.,0.529412 -aff_only fam_pl IP00FNW chr16:80639836:G:A 1,.,. 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.666667,.,. -aff_only fam_pl IP00FNY chr16:80639836:G:A 1,.,. 7 0.318 22 0.752 DB 483 9.0714 0.833 -0.4667 7 0.318 60 0 20.57 0.022 0.74 22.1 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.190708 0.178351 423 222 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.508772,.,. -aff_only fam_pl C0011JZ chr16:80639841:G:A 1,.,. 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.514286,.,. -aff_only fam_pl C0011K2 chr16:80639841:G:A 1,.,. 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.45098,.,. -aff_only fam_pl C0011K3 chr16:80639841:G:A 1,.,. 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.486486,.,. -aff_only fam_pl C0011KA chr16:80639841:G:A 1,.,1 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,51 0.52381,.,0.45098 -aff_only fam_pl IP00FNP chr16:80639841:G:A 1,.,1 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,35 0.483871,.,0.514286 -aff_only fam_pl IP00FNW chr16:80639841:G:A 1,.,. 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.666667,.,. -aff_only fam_pl IP00FNY chr16:80639841:G:A 1,.,. 7 0.318 22 0 DB 479 9.0714 0 -0.4667 7 0.318 60 0 20.63 0.07 0.693 22.19 MQRankSum A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.222883 0.179213 593 224 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.481481,.,. -aff_only fam_pl C0011JZ chr16:80834946:T:G 1,.,. 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.435897,.,. -aff_only fam_pl C0011K2 chr16:80834946:T:G 1,.,. 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.392857,.,. -aff_only fam_pl C0011K3 chr16:80834946:T:G 1,.,. 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.533333,.,. -aff_only fam_pl C0011KA chr16:80834946:T:G 1,.,1 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,56 0.392857,.,0.392857 -aff_only fam_pl IP00FNP chr16:80834946:T:G 1,.,1 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,39 0.6,.,0.435897 -aff_only fam_pl IP00FNW chr16:80834946:T:G 1,.,. 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.490196,.,. -aff_only fam_pl IP00FNY chr16:80834946:T:G 1,.,. 7 0.318 22 -0.806 DB 484 9.0714 2.88 -0.4667 7 0.318 60 0 13.07 0.217 0.863 23.42 MQRankSum G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1||| -1 0.283008 0.266613 871 480 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 72,.,. 0.486111,.,. -aff_only fam_pl C0011JZ chr16:81393010:G:GT 1,.,. 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,. 0.5625,.,. -aff_only fam_pl C0011K2 chr16:81393010:G:GT 1,.,. 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,. 0.692308,.,. -aff_only fam_pl C0011K3 chr16:81393010:G:GT 1,.,. 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.363636,.,. -aff_only fam_pl C0011KA chr16:81393010:G:GT 1,.,1 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,13 0.357143,.,0.692308 -aff_only fam_pl IP00FNP chr16:81393010:G:GT 1,.,1 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,16 0.818182,.,0.5625 -aff_only fam_pl IP00FNW chr16:81393010:G:GT 1,.,. 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,. 0.615385,.,. -aff_only fam_pl IP00FNY chr16:81393010:G:GT 1,.,. 7 0.318 22 0.16 DB 342 9.0714 15.728 -0.4377 7 0.318 59.94 0 8.46 0.491 1.837 5.1 MQRankSum T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1||| -1 0.433732 0.491475 1376 1103 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.583333,.,. -aff_only fam_pl C0011JZ chr16:82152710:G:T 1,.,. 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.5,.,. -aff_only fam_pl C0011K2 chr16:82152710:G:T 1,.,. 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.555556,.,. -aff_only fam_pl C0011K3 chr16:82152710:G:T 1,.,. 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.512195,.,. -aff_only fam_pl C0011KA chr16:82152710:G:T 1,.,1 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,54 0.5,.,0.555556 -aff_only fam_pl IP00FNP chr16:82152710:G:T 1,.,1 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,44 0.547945,.,0.5 -aff_only fam_pl IP00FNW chr16:82152710:G:T 1,.,. 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.517857,.,. -aff_only fam_pl IP00FNY chr16:82152710:G:T 1,.,. 7 0.318 22 -1.398 DB 501 9.0714 9.547 -0.4667 7 0.318 60 0 14.06 0.595 0.405 23.96 MQRankSum T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.170261 0.200132 303 265 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.425926,.,. -aff_only fam_pl C0011JZ chr16:82161091:TA:T 1,.,. 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 32,.,. 0.5625,.,. -aff_only fam_pl C0011K2 chr16:82161091:TA:T 1,.,. 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.478261,.,. -aff_only fam_pl C0011K3 chr16:82161091:TA:T 1,.,. 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 52,.,. 0.403846,.,. -aff_only fam_pl C0011KA chr16:82161091:TA:T 1,.,1 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,46 0.384615,.,0.478261 -aff_only fam_pl IP00FNP chr16:82161091:TA:T 1,.,1 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,32 0.446809,.,0.5625 -aff_only fam_pl IP00FNW chr16:82161091:TA:T 1,.,. 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 64,.,. 0.484375,.,. -aff_only fam_pl IP00FNY chr16:82161091:TA:T 1,.,. 7 0.318 22 0 DB 477 9.0714 8.803 -0.4667 7 0.318 60 0 14.51 -0.067 0.888 9.41 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES|||| -1 0.22923 0.284585 309 271 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.42029,.,. -aff_only fam_pl C0011JZ chr16:82294753:A:G 1,.,. 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.481481,.,. -aff_only fam_pl C0011K2 chr16:82294753:A:G 1,.,. 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.585366,.,. -aff_only fam_pl C0011K3 chr16:82294753:A:G 1,.,. 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.52381,.,. -aff_only fam_pl C0011KA chr16:82294753:A:G 1,.,1 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,41 0.611111,.,0.585366 -aff_only fam_pl IP00FNP chr16:82294753:A:G 1,.,1 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,27 0.4,.,0.481481 -aff_only fam_pl IP00FNW chr16:82294753:A:G 1,.,. 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.490566,.,. -aff_only fam_pl IP00FNY chr16:82294753:A:G 1,.,. 7 0.318 22 -1.442 DB 455 9.0714 7.721 -0.4667 7 0.318 60 0 12.15 0.508 0.425 23.56 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0416353 0.0542824 25 22 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.393443,.,. -aff_only fam_pl C0011JZ chr19:52133734:G:A 1,.,. 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.394737,.,. -aff_only fam_pl C0011K2 chr19:52133734:G:A 1,.,. 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.535714,.,. -aff_only fam_pl C0011K3 chr19:52133734:G:A 1,.,. 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.358974,.,. -aff_only fam_pl C0011KA chr19:52133734:G:A 1,.,1 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,28 0.405405,.,0.535714 -aff_only fam_pl IP00FNP chr19:52133734:G:A 1,.,1 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,38 0.285714,.,0.394737 -aff_only fam_pl IP00FNW chr19:52133734:G:A 1,.,. 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr19:52133734:G:A 1,.,. 7 0.318 22 0.996 DB 358 9.0714 22.608 -0.4667 7 0.318 48.84 1.86 10.89 0.438 1.647 -5.591 MQ A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874||||| -1 0.298587 0.278243 828 446 35 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.4,.,. -aff_only fam_pl C0011JZ chr19:52134334:TA:T 1,.,. 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,. 0.736842,.,. -aff_only fam_pl C0011K2 chr19:52134334:TA:T 1,.,. 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.535714,.,. -aff_only fam_pl C0011K3 chr19:52134334:TA:T 1,.,. 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 24,.,. 0.583333,.,. -aff_only fam_pl C0011KA chr19:52134334:TA:T 1,.,1 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,28 0.5625,.,0.535714 -aff_only fam_pl IP00FNP chr19:52134334:TA:T 1,.,1 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,19 0.464286,.,0.736842 -aff_only fam_pl IP00FNW chr19:52134334:TA:T 1,.,. 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.44,.,. -aff_only fam_pl IP00FNY chr19:52134334:TA:T 1,.,. 7 0.318 22 -0.496 346 9.0714 9.467 -0.5172 7 0.318 59.87 0 9.91 -0.266 0.35 5.73 MQRankSum -|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874||||| -1 0.300644 0.330881 704 588 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.722222,.,. -aff_only fam_pl C0011JZ chr19:52135776:G:T 1,.,. 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.37931,.,. -aff_only fam_pl C0011K2 chr19:52135776:G:T 1,.,. 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.422222,.,. -aff_only fam_pl C0011K3 chr19:52135776:G:T 1,.,. 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.578947,.,. -aff_only fam_pl C0011KA chr19:52135776:G:T 1,.,1 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,45 0.62069,.,0.422222 -aff_only fam_pl IP00FNP chr19:52135776:G:T 1,.,1 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,29 0.673469,.,0.37931 -aff_only fam_pl IP00FNW chr19:52135776:G:T 1,.,. 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.538462,.,. -aff_only fam_pl IP00FNY chr19:52135776:G:T 1,.,. 7 0.318 22 1.69 DB 418 9.0714 6.217 -0.4667 7 0.318 60 0 14.94 0.448 0.453 23.53 MQRankSum T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874||||| -1 0.291102 0.327437 1319 1031 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.491803,.,. -aff_only fam_pl C0011JZ chr19:52250589:G:A 1,.,. 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.655172,.,. -aff_only fam_pl C0011K2 chr19:52250589:G:A 1,.,. 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.511628,.,. -aff_only fam_pl C0011K3 chr19:52250589:G:A 1,.,. 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.295455,.,. -aff_only fam_pl C0011KA chr19:52250589:G:A 1,.,1 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,43 0.434783,.,0.511628 -aff_only fam_pl IP00FNP chr19:52250589:G:A 1,.,1 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,29 0.428571,.,0.655172 -aff_only fam_pl IP00FNW chr19:52250589:G:A 1,.,. 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.577778,.,. -aff_only fam_pl IP00FNY chr19:52250589:G:A 1,.,. 7 0.318 22 1.35 DB 445 9.0714 0.884 -0.4667 7 0.318 59.98 0 13.19 0.264 0.751 8.56 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.248148 0.229188 668 367 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 66,.,. 0.484848,.,. -aff_only fam_pl C0011JZ chr19:52250888:G:GATTCATGAATAC 1,.,. 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.517241,.,. -aff_only fam_pl C0011K2 chr19:52250888:G:GATTCATGAATAC 1,.,. 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.536585,.,. -aff_only fam_pl C0011K3 chr19:52250888:G:GATTCATGAATAC 1,.,. 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.384615,.,. -aff_only fam_pl C0011KA chr19:52250888:G:GATTCATGAATAC 1,.,1 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,41 0.588235,.,0.536585 -aff_only fam_pl IP00FNP chr19:52250888:G:GATTCATGAATAC 1,.,1 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,29 0.679245,.,0.517241 -aff_only fam_pl IP00FNW chr19:52250888:G:GATTCATGAATAC 1,.,. 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.543478,.,. -aff_only fam_pl IP00FNY chr19:52250888:G:GATTCATGAATAC 1,.,. 7 0.318 22 -0.199 DB 466 9.0714 0.416 -0.4667 7 0.318 60 0 23.13 -0.59 0.74 8.83 MQRankSum ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.242757 0.225191 577 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 64,.,. 0.5,.,. -aff_only fam_pl C0011JZ chr19:52250892:T:A 1,.,. 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.533333,.,. -aff_only fam_pl C0011K2 chr19:52250892:T:A 1,.,. 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.511111,.,. -aff_only fam_pl C0011K3 chr19:52250892:T:A 1,.,. 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.404762,.,. -aff_only fam_pl C0011KA chr19:52250892:T:A 1,.,1 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,45 0.588235,.,0.511111 -aff_only fam_pl IP00FNP chr19:52250892:T:A 1,.,1 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,30 0.62963,.,0.533333 -aff_only fam_pl IP00FNW chr19:52250892:T:A 1,.,. 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr19:52250892:T:A 1,.,. 7 0.318 22 0 DB 471 9.0714 0.848 -0.4667 7 0.318 60.03 0 20.67 -0.977 0.628 6.95 MQRankSum A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826||||| -1 0.243128 0.225295 578 313 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,. 0.528571,.,. -aff_only fam_pl C0011JZ chr19:53546001:C:CT 1,.,. 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.411765,.,. -aff_only fam_pl C0011K2 chr19:53546001:C:CT 1,.,. 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 19,.,. 0.631579,.,. -aff_only fam_pl C0011K3 chr19:53546001:C:CT 1,.,. 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.333333,.,. -aff_only fam_pl C0011KA chr19:53546001:C:CT 1,.,1 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,19 0.232558,.,0.631579 -aff_only fam_pl IP00FNP chr19:53546001:C:CT 1,.,1 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,34 0.216216,.,0.411765 -aff_only fam_pl IP00FNW chr19:53546001:C:CT 1,.,. 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.571429,.,. -aff_only fam_pl IP00FNY chr19:53546001:C:CT 1,.,. 7 0.318 22 0 DB 461 9.3779 11.346 -0.4667 7 0.318 60.05 0 10.25 -0.105 0.731 6.98 MQRankSum T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1||| -1 0.34934 0.373508 859 628 51 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 9,.,. 0.888889,.,. -aff_only fam_pl C0011JZ chr20:25742657:TA:T 1,.,. 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.0769231,.,. -aff_only fam_pl C0011K2 chr20:25742657:TA:T 1,.,. 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.179487,.,. -aff_only fam_pl C0011K3 chr20:25742657:TA:T 1,.,. 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 37,.,. 0.135135,.,. -aff_only fam_pl C0011KA chr20:25742657:TA:T 1,.,1 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,39 0.138889,.,0.179487 -aff_only fam_pl IP00FNP chr20:25742657:TA:T 1,.,1 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 77,.,39 0.181818,.,0.0769231 -aff_only fam_pl IP00FNW chr20:25742657:TA:T 1,.,. 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 64,.,. 0.15625,.,. -aff_only fam_pl IP00FNY chr20:25742657:TA:T 1,.,. 7 0.318 22 0.872 DB 554 9.0714 9.573 -0.4985 7 0.318 56.51 -6.102 4.1 1.54 1.37 -2.626 MQ -|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 78,.,. 0.192308,.,. -aff_only fam_pl C0011JZ chr20:25742669:G:A 1,.,. 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.0769231,.,. -aff_only fam_pl C0011K2 chr20:25742669:G:A 1,.,. 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.195122,.,. -aff_only fam_pl C0011K3 chr20:25742669:G:A 1,.,. 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.166667,.,. -aff_only fam_pl C0011KA chr20:25742669:G:A 1,.,1 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,41 0.147059,.,0.195122 -aff_only fam_pl IP00FNP chr20:25742669:G:A 1,.,1 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 74,.,39 0.175676,.,0.0769231 -aff_only fam_pl IP00FNW chr20:25742669:G:A 1,.,. 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 63,.,. 0.142857,.,. -aff_only fam_pl IP00FNY chr20:25742669:G:A 1,.,. 7 0.318 22 0.104 DB 548 9.0714 14.421 -0.5141 7 0.318 56.4 -6.102 4.03 0.242 1.367 -2.682 MQ A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503||||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 71,.,. 0.197183,.,. -aff_only fam_pl C0011JZ chr20:52482965:ATT:A 1,.,. 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,. 0.642857,.,. -aff_only fam_pl C0011K2 chr20:52482965:ATT:A 1,.,. 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,. 0.571429,.,. -aff_only fam_pl C0011K3 chr20:52482965:ATT:A 1,.,. 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.4,.,. -aff_only fam_pl C0011KA chr20:52482965:ATT:A 1,.,1 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 16,.,14 0.5625,.,0.571429 -aff_only fam_pl IP00FNP chr20:52482965:ATT:A 1,.,1 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 15,.,14 0.933333,.,0.642857 -aff_only fam_pl IP00FNW chr20:52482965:ATT:A 1,.,. 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 9,.,. 0.555556,.,. -aff_only fam_pl IP00FNY chr20:52482965:ATT:A 1,.,. 7 0.318 22 0.89 DB 405 0.5742 0 0.3714 7 0.318 60 0 15.88 0.366 0.707 8.98 MQRankSum -|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 -1 -1 -1 -1 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 11,.,. 0.636364,.,. -aff_only fam_pl C0011JZ chr20:54033324:C:CT 1,.,. 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 1,.,. -aff_only fam_pl C0011K2 chr20:54033324:C:CT 1,.,. 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 1,.,. -aff_only fam_pl C0011K3 chr20:54033324:C:CT 1,.,. 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 5,.,. 1,.,. -aff_only fam_pl C0011KA chr20:54033324:C:CT 1,.,1 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,7 0.571429,.,1 -aff_only fam_pl IP00FNP chr20:54033324:C:CT 1,.,1 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 1,.,7 1,.,1 -aff_only fam_pl IP00FNW chr20:54033324:C:CT 1,.,. 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 2,.,. 0.5,.,. -aff_only fam_pl IP00FNY chr20:54033324:C:CT 1,.,. 7 0.318 22 0.348 DB 258 2.9436 29.934 -0.1273 6 0.273 57.8 0 29.73 -0.589 0.036 0.33 MQRankSum T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,. 0.333333,.,. -aff_only fam_pl C0011JZ chr20:54066953:G:GT 1,.,. 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 14,.,. 0.428571,.,. -aff_only fam_pl C0011K2 chr20:54066953:G:GT 1,.,. 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.56,.,. -aff_only fam_pl C0011K3 chr20:54066953:G:GT 1,.,. 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.435897,.,. -aff_only fam_pl C0011KA chr20:54066953:G:GT 1,.,1 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,25 1,.,0.56 -aff_only fam_pl IP00FNP chr20:54066953:G:GT 1,.,1 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,14 0.289474,.,0.428571 -aff_only fam_pl IP00FNW chr20:54066953:G:GT 1,.,. 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.647059,.,. -aff_only fam_pl IP00FNY chr20:54066953:G:GT 1,.,. 7 0.318 22 0.566 424 6.4503 6.589 -0.3162 7 0.318 60 0 12.32 -0.02 1.008 8.23 MQRankSum T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES|||| -1 0.536377 0.607916 2722 2223 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.516129,.,. -aff_only fam_pl C0011JZ chr20:56003327:T:G 1,.,. 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.4,.,. -aff_only fam_pl C0011K2 chr20:56003327:T:G 1,.,. 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.5,.,. -aff_only fam_pl C0011K3 chr20:56003327:T:G 1,.,. 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.636364,.,. -aff_only fam_pl C0011KA chr20:56003327:T:G 1,.,1 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,28 0.48,.,0.5 -aff_only fam_pl IP00FNP chr20:56003327:T:G 1,.,1 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,25 0.73913,.,0.4 -aff_only fam_pl IP00FNW chr20:56003327:T:G 1,.,. 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 22,.,. 0.227273,.,. -aff_only fam_pl IP00FNY chr20:56003327:T:G 1,.,. 7 0.318 22 -0.935 DB 363 9.0714 3.606 -0.4667 7 0.318 60.27 0 13.91 0.759 0.47 5 MQRankSum G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.26186 0.310772 656 538 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.35,.,. -aff_only fam_pl C0011JZ chr20:57159924:TTTCC:T 1,.,. 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,. 0.470588,.,. -aff_only fam_pl C0011K2 chr20:57159924:TTTCC:T 1,.,. 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.48,.,. -aff_only fam_pl C0011K3 chr20:57159924:TTTCC:T 1,.,. 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.638889,.,. -aff_only fam_pl C0011KA chr20:57159924:TTTCC:T 1,.,1 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,25 0.36,.,0.48 -aff_only fam_pl IP00FNP chr20:57159924:TTTCC:T 1,.,1 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,17 0.457143,.,0.470588 -aff_only fam_pl IP00FNW chr20:57159924:TTTCC:T 1,.,. 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 27,.,. 0.37037,.,. -aff_only fam_pl IP00FNY chr20:57159924:TTTCC:T 1,.,. 7 0.318 22 0 DB 377 9.0714 1.121 -0.4667 7 0.318 59.65 0 18.3 0.094 0.604 6.39 MQRankSum -|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152||||| -1 0.417144 0.450964 1789 1316 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.576923,.,. -aff_only fam_pl C0011JZ chr20:57164080:G:A 1,.,. 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 44,.,. 0.431818,.,. -aff_only fam_pl C0011K2 chr20:57164080:G:A 1,.,. 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.435897,.,. -aff_only fam_pl C0011K3 chr20:57164080:G:A 1,.,. 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.489362,.,. -aff_only fam_pl C0011KA chr20:57164080:G:A 1,.,1 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,39 0.55,.,0.435897 -aff_only fam_pl IP00FNP chr20:57164080:G:A 1,.,1 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,44 0.339623,.,0.431818 -aff_only fam_pl IP00FNW chr20:57164080:G:A 1,.,. 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.52,.,. -aff_only fam_pl IP00FNY chr20:57164080:G:A 1,.,. 7 0.318 22 -1.066 DB 484 9.0714 3.527 -0.4667 7 0.318 60 0 12.29 0.658 0.769 23.65 MQRankSum A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152||||| -1 0.480499 0.492061 2472 1647 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.459016,.,. -aff_only fam_pl C0011JZ chr20:57246491:TGG:* 1,.,. 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,. 0.28,.,. -aff_only fam_pl C0011K2 chr20:57246491:TGG:* 1,.,. 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 30,.,. 0.533333,.,. -aff_only fam_pl C0011K3 chr20:57246491:TGG:* 1,.,. 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.530612,.,. -aff_only fam_pl C0011KA chr20:57246491:TGG:* 1,.,1 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 17,.,30 1,.,0.533333 -aff_only fam_pl IP00FNP chr20:57246491:TGG:* 1,.,1 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,25 0.304348,.,0.28 -aff_only fam_pl IP00FNW chr20:57246491:TGG:* 1,.,. 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 8,.,. 1,.,. -aff_only fam_pl IP00FNY chr20:57246491:TGG:* 1,.,. 7 0.318 22 0 DB 431 9.3779 7.165 -0.4667 7 0.318 59.75 0 9.47 -0.044 1.03 4.91 MQRankSum -1 0.372515 0.403123 1386 1055 2147483646 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.333333,.,. -aff_only fam_pl C0011JZ chr20:57311528:CA:C 1,.,. 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 6,.,. 1,.,. -aff_only fam_pl C0011K2 chr20:57311528:CA:C 1,.,. 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 6,.,. 1,.,. -aff_only fam_pl C0011K3 chr20:57311528:CA:C 1,.,. 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 1,.,. -aff_only fam_pl C0011KA chr20:57311528:CA:C 1,.,1 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 6,.,6 1,.,1 -aff_only fam_pl IP00FNP chr20:57311528:CA:C 1,.,1 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,6 1,.,1 -aff_only fam_pl IP00FNW chr20:57311528:CA:C 1,.,. 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 5,.,. 0.8,.,. -aff_only fam_pl IP00FNY chr20:57311528:CA:C 1,.,. 7 0.318 22 0 DB 192 4.4261 9.388 -0.221 7 0.318 60.31 0 20.36 0 0.077 5.11 MQRankSum -|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES|||| -1 0.387299 0.38905 271 190 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 3,.,. 1,.,. -aff_only fam_pl C0011JZ chr21:9830249:G:A 1,.,. 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 113,.,. 0.504425,.,. -aff_only fam_pl C0011K2 chr21:9830249:G:A 1,.,. 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 114,.,. 0.473684,.,. -aff_only fam_pl C0011K3 chr21:9830249:G:A 1,.,. 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 114,.,. 0.473684,.,. -aff_only fam_pl C0011KA chr21:9830249:G:A 1,.,1 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 81,.,114 0.518519,.,0.473684 -aff_only fam_pl IP00FNP chr21:9830249:G:A 1,.,1 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 193,.,113 0.274611,.,0.504425 -aff_only fam_pl IP00FNW chr21:9830249:G:A 1,.,. 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 89,.,. 0.157303,.,. -aff_only fam_pl IP00FNY chr21:9830249:G:A 1,.,. 7 0.318 22 1.94 DB 1399 9.0714 1.903 -0.6299 8 0.364 57.17 0.828 8 -0.978 0.653 -2.57 MQ A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES|||| -1 -1 -1 -1 -1 53 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 178,.,. 0.0955056,.,. -aff_only fam_pl C0011JZ chrX:134937170:G:GAAAAGA 1,.,. 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 21,.,. 0.428571,.,. -aff_only fam_pl C0011K2 chrX:134937170:G:GAAAAGA 1,.,. 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 13,.,. 0.230769,.,. -aff_only fam_pl C0011K3 chrX:134937170:G:GAAAAGA 1,.,. 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 10,.,. 0.8,.,. -aff_only fam_pl C0011KA chrX:134937170:G:GAAAAGA 1,.,1 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 25,.,13 0.36,.,0.230769 -aff_only fam_pl IP00FNP chrX:134937170:G:GAAAAGA 1,.,1 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,21 0.770833,.,0.428571 -aff_only fam_pl IP00FNW chrX:134937170:G:GAAAAGA 1,.,. 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 7,.,. 0.428571,.,. -aff_only fam_pl IP00FNY chrX:134937170:G:GAAAAGA 1,.,. 7 0.318 22 -0.14 DB 224 9.0714 0 -0.4671 7 0.318 25.64 0.134 24.15 0.845 1.041 -0.504 MQ AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1||| -1 0.483591 0.479371 32 19 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,. 0.608696,.,. -aff_only fam_pl C0011JZ chrX:134948600:C:T 1,.,. 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 62,.,. 0.483871,.,. -aff_only fam_pl C0011K2 chrX:134948600:C:T 1,.,. 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,. 0.410959,.,. -aff_only fam_pl C0011K3 chrX:134948600:C:T 1,.,. 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,. 0.679245,.,. -aff_only fam_pl C0011KA chrX:134948600:C:T 1,.,1 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 71,.,73 0.464789,.,0.410959 -aff_only fam_pl IP00FNP chrX:134948600:C:T 1,.,1 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,62 0.160714,.,0.483871 -aff_only fam_pl IP00FNW chrX:134948600:C:T 1,.,. 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 28,.,. 0.0714286,.,. -aff_only fam_pl IP00FNY chrX:134948600:C:T 1,.,. 7 0.318 22 0.389 DB 504 9.0714 193.058 -0.4667 7 0.318 50.9 -5.098 15.19 -2.875 4.094 -257.2 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.420312 0.404793 2 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.139535,.,. -aff_only fam_pl C0011JZ chrX:134948607:G:A 1,.,. 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.521739,.,. -aff_only fam_pl C0011K2 chrX:134948607:G:A 1,.,. 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 82,.,. 0.439024,.,. -aff_only fam_pl C0011K3 chrX:134948607:G:A 1,.,. 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 57,.,. 0.684211,.,. -aff_only fam_pl C0011KA chrX:134948607:G:A 1,.,1 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,82 0.478261,.,0.439024 -aff_only fam_pl IP00FNP chrX:134948607:G:A 1,.,1 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 70,.,69 0.342857,.,0.521739 -aff_only fam_pl IP00FNW chrX:134948607:G:A 1,.,. 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 31,.,. 0.290323,.,. -aff_only fam_pl IP00FNY chrX:134948607:G:A 1,.,. 7 0.318 22 -0.104 DB 548 9.0714 106.681 -0.4667 7 0.318 50.71 -5.313 19.31 -3.049 4.047 -85.24 ReadPosRankSum A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.421811 0.406186 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.34,.,. -aff_only fam_pl C0011JZ chrX:134948616:C:G 1,.,. 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 78,.,. 0.551282,.,. -aff_only fam_pl C0011K2 chrX:134948616:C:G 1,.,. 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 86,.,. 0.476744,.,. -aff_only fam_pl C0011K3 chrX:134948616:C:G 1,.,. 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,. 0.707692,.,. -aff_only fam_pl C0011KA chrX:134948616:C:G 1,.,1 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 78,.,86 0.512821,.,0.476744 -aff_only fam_pl IP00FNP chrX:134948616:C:G 1,.,1 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 101,.,78 0.544554,.,0.551282 -aff_only fam_pl IP00FNW chrX:134948616:C:G 1,.,. 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.424242,.,. -aff_only fam_pl IP00FNY chrX:134948616:C:G 1,.,. 7 0.318 22 -0.522 DB 613 9.0714 100.79 -0.4667 7 0.318 48.97 -6.059 21.77 -2.647 3.591 -77.59 FS G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.429463 0.416219 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 55,.,. 0.436364,.,. -aff_only fam_pl C0011JZ chrX:134948621:G:A 1,.,. 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 78,.,. 0.576923,.,. -aff_only fam_pl C0011K2 chrX:134948621:G:A 1,.,. 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 91,.,. 0.483516,.,. -aff_only fam_pl C0011K3 chrX:134948621:G:A 1,.,. 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 73,.,. 0.712329,.,. -aff_only fam_pl C0011KA chrX:134948621:G:A 1,.,1 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 79,.,91 0.531646,.,0.483516 -aff_only fam_pl IP00FNP chrX:134948621:G:A 1,.,1 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 114,.,78 0.578947,.,0.576923 -aff_only fam_pl IP00FNW chrX:134948621:G:A 1,.,. 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.457143,.,. -aff_only fam_pl IP00FNY chrX:134948621:G:A 1,.,. 7 0.318 22 -0.303 DB 648 9.0714 94.1 -0.4667 7 0.318 47.7 -6.004 23.19 -1.462 3.563 -69.37 FS A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.432844 0.420593 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 61,.,. 0.47541,.,. -aff_only fam_pl C0011JZ chrX:134948627:G:T 1,.,. 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.575,.,. -aff_only fam_pl C0011K2 chrX:134948627:G:T 1,.,. 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 97,.,. 0.494845,.,. -aff_only fam_pl C0011K3 chrX:134948627:G:T 1,.,. 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 75,.,. 0.733333,.,. -aff_only fam_pl C0011KA chrX:134948627:G:T 1,.,1 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 81,.,97 0.530864,.,0.494845 -aff_only fam_pl IP00FNP chrX:134948627:G:T 1,.,1 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 134,.,80 0.604478,.,0.575 -aff_only fam_pl IP00FNW chrX:134948627:G:T 1,.,. 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.55,.,. -aff_only fam_pl IP00FNY chrX:134948627:G:T 1,.,. 7 0.318 22 0 DB 689 9.0714 77.771 -0.4667 7 0.318 46.64 -6.154 23.69 -0.588 3.175 -49.84 FS T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.433457 0.422021 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 65,.,. 0.538462,.,. -aff_only fam_pl C0011JZ chrX:134948631:T:C 1,.,. 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.5875,.,. -aff_only fam_pl C0011K2 chrX:134948631:T:C 1,.,. 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 97,.,. 0.494845,.,. -aff_only fam_pl C0011K3 chrX:134948631:T:C 1,.,. 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 76,.,. 0.736842,.,. -aff_only fam_pl C0011KA chrX:134948631:T:C 1,.,1 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 81,.,97 0.54321,.,0.494845 -aff_only fam_pl IP00FNP chrX:134948631:T:C 1,.,1 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 149,.,80 0.630872,.,0.5875 -aff_only fam_pl IP00FNW chrX:134948631:T:C 1,.,. 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,. 0.586957,.,. -aff_only fam_pl IP00FNY chrX:134948631:T:C 1,.,. 7 0.318 22 0 DB 714 9.0714 73.518 -0.4667 7 0.318 45.91 -6.184 24.31 0.148 3.066 -45.68 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434103 0.42281 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 68,.,. 0.558824,.,. -aff_only fam_pl C0011JZ chrX:134948635:A:C 1,.,. 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 81,.,. 0.604938,.,. -aff_only fam_pl C0011K2 chrX:134948635:A:C 1,.,. 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 97,.,. 0.505155,.,. -aff_only fam_pl C0011K3 chrX:134948635:A:C 1,.,. 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 80,.,. 0.7625,.,. -aff_only fam_pl C0011KA chrX:134948635:A:C 1,.,1 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 82,.,97 0.560976,.,0.505155 -aff_only fam_pl IP00FNP chrX:134948635:A:C 1,.,1 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 155,.,81 0.625806,.,0.604938 -aff_only fam_pl IP00FNW chrX:134948635:A:C 1,.,. 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.604167,.,. -aff_only fam_pl IP00FNY chrX:134948635:A:C 1,.,. 7 0.318 22 0.035 DB 735 9.0714 66.587 -0.4667 7 0.318 45.42 -6.252 23.83 -0.345 2.865 -38.84 MQ C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.434903 0.42377 3 2 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 75,.,. 0.6,.,. -aff_only fam_pl C0011JZ chrX:134948709:C:T 1,.,. 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 118,.,. 0.127119,.,. -aff_only fam_pl C0011K2 chrX:134948709:C:T 1,.,. 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 124,.,. 0.185484,.,. -aff_only fam_pl C0011K3 chrX:134948709:C:T 1,.,. 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 121,.,. 0.165289,.,. -aff_only fam_pl C0011KA chrX:134948709:C:T 1,.,1 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 124,.,124 0.177419,.,0.185484 -aff_only fam_pl IP00FNP chrX:134948709:C:T 1,.,1 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 315,.,118 0.190476,.,0.127119 -aff_only fam_pl IP00FNW chrX:134948709:C:T 1,.,. 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,. 0.275362,.,. -aff_only fam_pl IP00FNY chrX:134948709:C:T 1,.,. 7 0.318 22 2.11 1113 9.0714 22.023 -0.4667 7 0.318 37.91 2.79 5.06 -0.122 0.396 -10.5 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.293792 0.302233 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 122,.,. 0.196721,.,. -aff_only fam_pl C0011JZ chrX:134948718:C:T 1,.,. 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 119,.,. 0.117647,.,. -aff_only fam_pl C0011K2 chrX:134948718:C:T 1,.,. 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 122,.,. 0.172131,.,. -aff_only fam_pl C0011K3 chrX:134948718:C:T 1,.,. 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 122,.,. 0.163934,.,. -aff_only fam_pl C0011KA chrX:134948718:C:T 1,.,1 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 125,.,122 0.184,.,0.172131 -aff_only fam_pl IP00FNP chrX:134948718:C:T 1,.,1 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 286,.,119 0.199301,.,0.117647 -aff_only fam_pl IP00FNW chrX:134948718:C:T 1,.,. 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 68,.,. 0.294118,.,. -aff_only fam_pl IP00FNY chrX:134948718:C:T 1,.,. 7 0.318 22 0.15 DB 1082 9.0714 21.995 -0.4667 7 0.318 37.69 2.47 5.23 0.147 0.466 -10.47 MQ T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.287569 0.296629 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 119,.,. 0.210084,.,. -aff_only fam_pl C0011JZ chrX:134948824:G:A 1,.,. 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 97,.,. 0.237113,.,. -aff_only fam_pl C0011K2 chrX:134948824:G:A 1,.,. 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 111,.,. 0.225225,.,. -aff_only fam_pl C0011K3 chrX:134948824:G:A 1,.,. 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 84,.,. 0.214286,.,. -aff_only fam_pl C0011KA chrX:134948824:G:A 1,.,1 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 88,.,111 0.227273,.,0.225225 -aff_only fam_pl IP00FNP chrX:134948824:G:A 1,.,1 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 132,.,97 0.257576,.,0.237113 -aff_only fam_pl IP00FNW chrX:134948824:G:A 1,.,. 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.354167,.,. -aff_only fam_pl IP00FNY chrX:134948824:G:A 1,.,. 7 0.318 22 2.06 DB 752 9.0714 0.606 -0.4667 7 0.318 28.95 0.666 4.61 0.497 0.787 -9.321 MQ A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.374159 0.36645 1 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 88,.,. 0.318182,.,. -aff_only fam_pl C0011JZ chrX:134949149:A:G 1,.,. 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 43,.,. 0.325581,.,. -aff_only fam_pl C0011K2 chrX:134949149:A:G 1,.,. 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 56,.,. 0.267857,.,. -aff_only fam_pl C0011K3 chrX:134949149:A:G 1,.,. 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.413793,.,. -aff_only fam_pl C0011KA chrX:134949149:A:G 1,.,1 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,56 0.297872,.,0.267857 -aff_only fam_pl IP00FNP chrX:134949149:A:G 1,.,1 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,43 0.411765,.,0.325581 -aff_only fam_pl IP00FNW chrX:134949149:A:G 1,.,. 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.333333,.,. -aff_only fam_pl IP00FNY chrX:134949149:A:G 1,.,. 7 0.318 22 -0.514 DB 387 9.0714 3.677 -0.4667 7 0.318 27.22 -0.372 6.81 1.72 0.929 -10.09 MQ G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1||| -1 0.407801 0.401294 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.555556,.,. -aff_only fam_pl C0011JZ chrX:140078339:T:C 1,.,. 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 42,.,. 0.261905,.,. -aff_only fam_pl C0011K2 chrX:140078339:T:C 1,.,. 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 54,.,. 0.314815,.,. -aff_only fam_pl C0011K3 chrX:140078339:T:C 1,.,. 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.6,.,. -aff_only fam_pl C0011KA chrX:140078339:T:C 1,.,1 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,54 0.333333,.,0.314815 -aff_only fam_pl IP00FNP chrX:140078339:T:C 1,.,1 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,42 0.333333,.,0.261905 -aff_only fam_pl IP00FNW chrX:140078339:T:C 1,.,. 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 26,.,. 0.384615,.,. -aff_only fam_pl IP00FNY chrX:140078339:T:C 1,.,. 7 0.318 22 1.05 406 9.0714 1.994 -0.4713 7 0.318 57.31 0.195 9.9 0.441 0.577 -2.305 MQ C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES|||| -1 0.146135 0.141665 0 0 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 49,.,. 0.469388,.,. -aff_only fam_pl C0011JZ chrX:140780417:A:G 1,.,. 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 35,.,. 0.114286,.,. -aff_only fam_pl C0011K2 chrX:140780417:A:G 1,.,. 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 36,.,. 0.0833333,.,. -aff_only fam_pl C0011K3 chrX:140780417:A:G 1,.,. 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 18,.,. 0.222222,.,. -aff_only fam_pl C0011KA chrX:140780417:A:G 1,.,1 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 23,.,36 0.173913,.,0.0833333 -aff_only fam_pl IP00FNP chrX:140780417:A:G 1,.,1 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,35 0.0882353,.,0.114286 -aff_only fam_pl IP00FNW chrX:140780417:A:G 1,.,. 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 20,.,. 0.35,.,. -aff_only fam_pl IP00FNY chrX:140780417:A:G 1,.,. 7 0.318 22 -1.672 DB 307 9.0714 13.067 -0.4558 7 0.318 55.06 -2.028 4.2 1.22 0.179 -2.505 MQ G|intergenic_variant|MODIFIER||||||||||||||||||||||||| -1 0.0578861 0.0275727 0 0 64 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 29,.,. 0.241379,.,. -aff_only fam_pl C0011JZ chrX:140785739:A:C 1,.,. 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.342105,.,. -aff_only fam_pl C0011K2 chrX:140785739:A:C 1,.,. 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 47,.,. 0.212766,.,. -aff_only fam_pl C0011K3 chrX:140785739:A:C 1,.,. 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.5,.,. -aff_only fam_pl C0011KA chrX:140785739:A:C 1,.,1 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,47 0.1,.,0.212766 -aff_only fam_pl IP00FNP chrX:140785739:A:C 1,.,1 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 72,.,38 0.111111,.,0.342105 -aff_only fam_pl IP00FNW chrX:140785739:A:C 1,.,. 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.176471,.,. -aff_only fam_pl IP00FNY chrX:140785739:A:C 1,.,. 7 0.318 22 -0.057 DB 424 9.0714 1.077 -0.4667 7 0.318 57.28 -3.626 6.21 -0.446 0.805 -2.108 MQ C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)| -1 0.0596689 0.0522111 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.153846,.,. -aff_only fam_pl C0011JZ chrX:140785741:A:C 1,.,. 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 39,.,. 0.333333,.,. -aff_only fam_pl C0011K2 chrX:140785741:A:C 1,.,. 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 48,.,. 0.208333,.,. -aff_only fam_pl C0011K3 chrX:140785741:A:C 1,.,. 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 34,.,. 0.5,.,. -aff_only fam_pl C0011KA chrX:140785741:A:C 1,.,1 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,48 0.0980392,.,0.208333 -aff_only fam_pl IP00FNP chrX:140785741:A:C 1,.,1 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 69,.,39 0.115942,.,0.333333 -aff_only fam_pl IP00FNW chrX:140785741:A:C 1,.,. 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 33,.,. 0.181818,.,. -aff_only fam_pl IP00FNY chrX:140785741:A:C 1,.,. 7 0.318 22 -1.394 DB 422 9.0714 1.692 -0.4667 7 0.318 57.32 -3.694 6.25 -0.164 0.822 -2.102 MQRankSum C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)| -1 0.103136 0.0958019 4 0 14 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 38,.,. 0.157895,.,. -aff_only fam_pl C0011JZ chrX:140785855:A:G 1,.,. 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 45,.,. 0.377778,.,. -aff_only fam_pl C0011K2 chrX:140785855:A:G 1,.,. 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 40,.,. 0.3,.,. -aff_only fam_pl C0011K3 chrX:140785855:A:G 1,.,. 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 41,.,. 0.536585,.,. -aff_only fam_pl C0011KA chrX:140785855:A:G 1,.,1 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 46,.,40 0.23913,.,0.3 -aff_only fam_pl IP00FNP chrX:140785855:A:G 1,.,1 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 53,.,45 0.245283,.,0.377778 -aff_only fam_pl IP00FNW chrX:140785855:A:G 1,.,. 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 50,.,. 0.36,.,. -aff_only fam_pl IP00FNY chrX:140785855:A:G 1,.,. 7 0.318 22 0.845 DB 435 9.0714 2.507 -0.4667 7 0.318 57.08 -0.85 8.93 0.412 0.555 -2.355 MQ G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1||| -1 0.155131 0.149268 2 1 47 C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY 51,.,. 0.411765,.,. diff --git a/example of results/PL_family_WGS_slivar_1664358140/res.vcf b/example of results/PL_family_WGS_slivar_1664358140/res.vcf deleted file mode 100644 index 7c225db..0000000 --- a/example of results/PL_family_WGS_slivar_1664358140/res.vcf +++ /dev/null @@ -1,305 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER=<ID=PASS,Description="All filters passed"> -##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> -##FILTER=<ID=LowQual,Description="Low quality"> -##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.5351 <= x < -0.4741"> -##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -20794.8907"> -##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -20794.8907 <= x < -4.5351"> -##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39178.8364"> -##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39178.8364 <= x < -2.9039"> -##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> -##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> -##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> -##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> -##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-0-gcfedb67,Date="Tue Aug 04 18:41:02 CEST 2020",Epoch=1596559262546,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/dev/shm/hs37d5_all_chr.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.g.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-indel-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-vqsr.vcf.gz --truth-sensitivity-filter-level 99.0 --mode INDEL --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:50:15 PM CEST"> -##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.recal --tranches-file /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.tranches --output /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-snp-vqsr.vcf.gz --truth-sensitivity-filter-level 99.5 --mode SNP --variant /pasteur/sonic/scratch/users/fcliquet/vcf/Dyslexia.gatk-no-vqsr.vcf.gz --reference references/GRCh37/chr/hs37d5.fa --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 16, 2021 12:31:29 PM CEST"> -##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path /local/scratch/tmp/38734053_1//Dyslexia.chr1.1-1000000 --overwrite-existing-genomicsdb-workspace true --batch-size 50 --consolidate true --sample-name-map /local/scratch/tmp/38734053_1/sample.map --reader-threads 1 --intervals chr1:1-1000000 --interval-padding 500 --tmp-dir /local/scratch/tmp/38734053_1//tmp/ --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --validate-sample-name-map false --merge-input-intervals false --max-num-intervals-to-import-in-parallel 1 --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.8.1",Date="September 15, 2021 3:11:49 PM CEST"> -##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /local/scratch/tmp/38743216_1/Dyslexia.chr1.1-1000000.genotyped.vcf.gz --only-output-calls-starting-in-intervals true --dbsnp /pasteur/zeus/projets/p02/ghfc_wgs_zeus/tools/ngs-workflow/references/GRCh37/chr/gatk-bundle/dbsnp_138.hg19.vcf.gz --variant gendb:///local/scratch/tmp/38743216_1//Dyslexia.chr1.1-1000000 --intervals chr1:1-1000000 --reference references/GRCh37/chr/hs37d5.fa --annotation-group StandardAnnotation --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.8.1",Date="September 15, 2021 3:30:43 PM CEST"> -##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --standard-min-confidence-threshold-for-calling 10.0 --output /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/VARIANT_C0011JY/C0011JY_hs37d5_BOTH_01.HC.temp.g.vcf --intervals /ccc/work/cont007/fg/fg/biobank/by-soft/varscope/hs37d5/WG_hs37d5_regions.target_split_bed/01_overlap.bed --input /ccc/scratch/cont007/fg0058/fg0058/projet_AUTISMEWG_592/ANALYSE/ANALYSE_A592_C0011JY_H72NKCCX2_1_hs37d5/MAPPING_C0011JY/reliable.realign.recal/A592_DA_C0011JY_H72NKCCX2_hs37d5_MERGE_PE_1_01.reliable.realign.recal.bam --reference /dev/shm/hs37d5_all_chr.fasta --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.1.0.0,Date="August 4, 2020 4:14:40 PM CEST"> -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> -##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> -##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> -##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model"> -##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"> -##bcftools_normCommand=norm -m - -w 10000 -f references/GRCh37/chr/hs37d5.fa; Date=Wed Sep 15 15:31:06 2021 -##bcftools_normVersion=1.12+htslib-1.12 -##contig=<ID=chr1,length=249250621> -##contig=<ID=chr2,length=243199373> -##contig=<ID=chr3,length=198022430> -##contig=<ID=chr4,length=191154276> -##contig=<ID=chr5,length=180915260> -##contig=<ID=chr6,length=171115067> -##contig=<ID=chr7,length=159138663> -##contig=<ID=chr8,length=146364022> -##contig=<ID=chr9,length=141213431> -##contig=<ID=chr10,length=135534747> -##contig=<ID=chr11,length=135006516> -##contig=<ID=chr12,length=133851895> -##contig=<ID=chr13,length=115169878> -##contig=<ID=chr14,length=107349540> -##contig=<ID=chr15,length=102531392> -##contig=<ID=chr16,length=90354753> -##contig=<ID=chr17,length=81195210> -##contig=<ID=chr18,length=78077248> -##contig=<ID=chr19,length=59128983> -##contig=<ID=chr20,length=63025520> -##contig=<ID=chr21,length=48129895> -##contig=<ID=chr22,length=51304566> -##contig=<ID=chrX,length=155270560> -##contig=<ID=chrY,length=59373566> -##contig=<ID=chrMT,length=16569> -##contig=<ID=GL000207.1,length=4262> -##contig=<ID=GL000226.1,length=15008> -##contig=<ID=GL000229.1,length=19913> -##contig=<ID=GL000231.1,length=27386> -##contig=<ID=GL000210.1,length=27682> -##contig=<ID=GL000239.1,length=33824> -##contig=<ID=GL000235.1,length=34474> -##contig=<ID=GL000201.1,length=36148> -##contig=<ID=GL000247.1,length=36422> -##contig=<ID=GL000245.1,length=36651> -##contig=<ID=GL000197.1,length=37175> -##contig=<ID=GL000203.1,length=37498> -##contig=<ID=GL000246.1,length=38154> -##contig=<ID=GL000249.1,length=38502> -##contig=<ID=GL000196.1,length=38914> -##contig=<ID=GL000248.1,length=39786> -##contig=<ID=GL000244.1,length=39929> -##contig=<ID=GL000238.1,length=39939> -##contig=<ID=GL000202.1,length=40103> -##contig=<ID=GL000234.1,length=40531> -##contig=<ID=GL000232.1,length=40652> -##contig=<ID=GL000206.1,length=41001> -##contig=<ID=GL000240.1,length=41933> -##contig=<ID=GL000236.1,length=41934> -##contig=<ID=GL000241.1,length=42152> -##contig=<ID=GL000243.1,length=43341> -##contig=<ID=GL000242.1,length=43523> -##contig=<ID=GL000230.1,length=43691> -##contig=<ID=GL000237.1,length=45867> -##contig=<ID=GL000233.1,length=45941> -##contig=<ID=GL000204.1,length=81310> -##contig=<ID=GL000198.1,length=90085> -##contig=<ID=GL000208.1,length=92689> -##contig=<ID=GL000191.1,length=106433> -##contig=<ID=GL000227.1,length=128374> -##contig=<ID=GL000228.1,length=129120> -##contig=<ID=GL000214.1,length=137718> -##contig=<ID=GL000221.1,length=155397> -##contig=<ID=GL000209.1,length=159169> -##contig=<ID=GL000218.1,length=161147> -##contig=<ID=GL000220.1,length=161802> -##contig=<ID=GL000213.1,length=164239> -##contig=<ID=GL000211.1,length=166566> -##contig=<ID=GL000199.1,length=169874> -##contig=<ID=GL000217.1,length=172149> -##contig=<ID=GL000216.1,length=172294> -##contig=<ID=GL000215.1,length=172545> -##contig=<ID=GL000205.1,length=174588> -##contig=<ID=GL000219.1,length=179198> -##contig=<ID=GL000224.1,length=179693> -##contig=<ID=GL000223.1,length=180455> -##contig=<ID=GL000195.1,length=182896> -##contig=<ID=GL000212.1,length=186858> -##contig=<ID=GL000222.1,length=186861> -##contig=<ID=GL000200.1,length=187035> -##contig=<ID=GL000193.1,length=189789> -##contig=<ID=GL000194.1,length=191469> -##contig=<ID=GL000225.1,length=211173> -##contig=<ID=GL000192.1,length=547496> -##contig=<ID=NC_007605,length=171823> -##contig=<ID=hs37d5,length=35477943> -##reference=file:///dev/shm/hs37d5_all_chr.fasta -##source=ApplyVQSR -##source=GenomicsDBImport -##source=GenotypeGVCFs -##source=HaplotypeCaller -##source=SelectVariants -##bcftools_normCommand=norm -m - -w 1000 -c s -f references/GRCh37/chr/hs37d5.fa --threads 3 -Oz -o /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/splitted/Dyslexia.gatk-vqsr.splitted.chr1.1-10000000.norm.vcf.gz; Date=Thu Sep 16 12:54:23 2021 -##VEP="v104" time="2021-09-16 12:54:40" cache="tools/ensembl-vep-104.3/data/homo_sapiens/104_GRCh37" ensembl-variation=104.20f5335 ensembl-funcgen=104.f1c7762 ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2" -##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET"> -##INFO=<ID=cadd_phred,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=cadd_phred_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_af_all,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_af_all_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_af_nfe,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_af_nfe_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_all,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_all_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_nfe,Number=1,Type=Float,Description="field from from gnotate VCF"> -##INFO=<ID=gno_non_neuro_nhomalt_nfe_filter,Number=0,Type=Flag,Description="non-passing flag in gnotate source VCF"> -##INFO=<ID=aff_only,Number=.,Type=String,Description="added by slivar with expression: 'fam.every(find_het_aff_hom_ref_unaff)' from Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz"> -##INFO=<ID=impactful,Number=0,Type=Flag,Description="variant is impactful according to slivar and impacts added by VEP/snpEff/bcftools (https://github.com/brentp/slivar/wiki/impactful)"> -##INFO=<ID=genic,Number=0,Type=Flag,Description="variant is genic according to slivar and impacts added by VEP/snpEff/bcftools (https://github.com/brentp/slivar/wiki/impactful)"> -##INFO=<ID=highest_impact_order,Number=1,Type=Integer,Description="impact order (lower is higher) of this variant across all genes and transcripts it overlaps. this integer can be used as a look into the order list to get the actual impact"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT C0011JY C0011JZ C0011K1 C0011K2 C0011K3 C0011K5 C0011KA C0011KB IP00FNP IP00FNW IP00FNY -chr1 142674001 rs138979035 C T 2248.45 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.31;DB;DP=1223;ExcessHet=9.0714;FS=8.045;InbreedingCoeff=-0.467;MLEAC=7;MLEAF=0.318;MQ=42.32;MQRankSum=-2.342;QD=2.86;ReadPosRankSum=0.256;SOR=1.492;VQSLOD=-4.51;culprit=MQ;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000369381|lincRNA||6/8|ENST00000369381.2:n.2507+18961G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000400755|lincRNA||4/4|ENST00000400755.3:n.245+3394C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000411746|lincRNA||2/3|ENST00000411746.1:n.517-50178C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|Transcript|ENST00000446205|lincRNA||4/5|ENST00000446205.2:n.401-16863C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|Transcript|ENST00000610091|lincRNA||11/13|ENST00000610091.1:n.3560+18961G>A|||||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.303041;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.339451;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:128,0:128:22:.:.:0,22,3605:. 0/1:86,15:101:99:.:.:276,0,2582:. 0/0:87,0:87:99:.:.:0,120,1800:. 0/1:93,9:102:25:.:.:25,0,2854:. 0|1:77,8:85:63:0|1:142673986_C_A:63,0,3145:142673986 0/0:93,0:93:99:.:.:0,120,1800:. 0/1:102,26:128:99:.:.:571,0,2973:. 0/0:113,9:122:35:.:.:0,35,3384:. 0/1:114,43:157:99:.:.:921,0,3356:. 0/1:52,9:61:99:.:.:111,0,1480:. 0/1:135,18:153:99:.:.:299,0,3793:. -chr1 146487361 . ACC * 230.29 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.103;DP=397;ExcessHet=20.6;FS=13.198;InbreedingCoeff=-0.8858;MLEAC=7;MLEAF=0.318;MQ=29.75;MQRankSum=1.31;QD=0.69;ReadPosRankSum=1.64;SOR=1.251;VQSLOD=-1.591;culprit=MQ;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=2147483646;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,2:42:3:.:.:0,3,2172:. 0/1:10,8:24:99:.:.:397,0,378:. 0/0:15,4:28:99:.:.:370,109,701:. 0|1:33,6:39:99:0|1:146487360_AACC_A:153,0,1394:146487360 0|1:34,3:37:66:0|1:146487360_AACC_A:66,0,1598:146487360 0/0:11,5:22:12:.:.:322,12,438:. 0/1:23,4:30:50:.:.:228,0,939:. 0/0:10,4:22:99:.:.:423,121,502:. 0/1:18,13:43:25:.:.:649,0,705:. 0/1:12,12:27:99:.:.:509,0,438:. 0|1:43,20:63:99:0|1:146487360_AACC_A:710,0,1681:146487360 -chr2 53605544 rs141200257;rs60803496 T TTTTTA 6326.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.754;DB;DP=504;ExcessHet=9.0714;FS=6.984;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.09;MQRankSum=0;QD=21.37;ReadPosRankSum=-0.352;SOR=0.727;VQSLOD=8.51;culprit=MQRankSum;CSQ=TTTTA|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.453228;gno_non_neuro_af_nfe=0.357854;gno_non_neuro_nhomalt_all=2369;gno_non_neuro_nhomalt_nfe=819;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,101,1281 0/1:10,11:21:99:429,0,566 0/0:38,0:38:99:0,100,1272 0/1:15,16:31:99:626,0,851 0/1:21,17:38:99:690,0,1186 0/0:38,0:38:99:0,99,1217 0/1:15,18:33:99:743,0,826 0/0:42,0:42:99:0,107,1410 0/1:22,33:55:99:1419,0,1196 0/1:20,25:45:99:1008,0,1073 0/1:37,36:73:99:1429,0,2048 -chr2 53606631 rs1402903 C T 5457.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.23;DB;DP=519;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.71;ReadPosRankSum=0.429;SOR=0.7;VQSLOD=23.52;culprit=MQRankSum;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.454644;gno_non_neuro_af_nfe=0.358489;gno_non_neuro_nhomalt_all=2456;gno_non_neuro_nhomalt_nfe=857;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1321 0/1:27,24:51:99:661,0,735 0/0:35,0:35:99:0,99,1166 0/1:16,22:38:99:651,0,432 0/1:24,28:52:99:777,0,638 0/0:35,0:35:99:0,99,1370 0/1:19,17:36:99:483,0,542 0/0:42,0:42:99:0,99,1399 0/1:31,30:61:99:859,0,754 0/1:32,30:62:99:857,0,711 0/1:30,41:71:99:1187,0,719 -chr2 53611448 rs11125488 T A 5175.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=484;ExcessHet=9.0714;FS=0.388;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.87;ReadPosRankSum=-0.338;SOR=0.726;VQSLOD=23.79;culprit=MQRankSum;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.457699;gno_non_neuro_af_nfe=0.358439;gno_non_neuro_nhomalt_all=2490;gno_non_neuro_nhomalt_nfe=851;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1176 0/1:17,17:34:99:429,0,486 0/0:38,0:38:99:0,102,1205 0/1:17,27:44:99:766,0,428 0/1:18,29:47:99:857,0,461 0/0:34,0:34:99:0,99,1176 0/1:15,19:34:99:546,0,386 0/0:28,0:28:84:0,84,963 0/1:36,28:64:99:778,0,1059 0/1:32,26:58:99:712,0,928 0/1:29,38:67:99:1105,0,807 -chr2 55855379 rs11298008 CA C 609.37 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.566;DB;DP=226;ExcessHet=5.8108;FS=6.666;InbreedingCoeff=-0.3786;MLEAC=6;MLEAF=0.273;MQ=59.92;MQRankSum=0;QD=7.71;ReadPosRankSum=0.366;SOR=1.483;VQSLOD=5.55;culprit=MQRankSum;CSQ=-|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.581573;gno_non_neuro_af_nfe=0.577764;gno_non_neuro_nhomalt_all=1048;gno_non_neuro_nhomalt_nfe=734;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:27,0:27:0:.:.:0,0,469:. 0/1:3,6:9:34:.:.:95,0,34:. 0/0:38,0:38:0:.:.:0,0,655:. 1/0:1,6:9:13:.:.:109,13,20:. 0/1:5,7:12:65:.:.:106,0,65:. 0/0:4,0:7:19:.:.:19,39,173:. 0|1:4,10:14:47:0|1:55855379_CA_C:140,0,47:55855379 0/0:5,0:12:64:.:.:104,118,250:. 0/1:3,1:5:3:.:.:3,0,78:. 1/0:1,4:6:3:.:.:42,3,33:. 0/1:4,3:7:10:.:.:10,0,71:. -chr2 61475320 rs11339335;rs375683015 CA C 668.17 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=252;ExcessHet=4.3978;FS=0;InbreedingCoeff=-0.2173;MLEAC=7;MLEAF=0.318;MQ=57.71;MQRankSum=0;QD=9.68;ReadPosRankSum=0.199;SOR=0.618;VQSLOD=1.8;culprit=MQRankSum;CSQ=-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000398571|protein_coding||49/79|ENST00000398571.2:c.6394+325del|||||||||-1||HGNC|20066|YES|CCDS42686.1|||,-|intron_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000453734|protein_coding||11/23|ENST00000453734.1:c.1228+325del|||||||||-1|cds_start_NF|HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000463046|retained_intron||3/27|ENST00000463046.1:n.282+325del|||||||||-1||HGNC|20066|||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|USP34|ENSG00000115464|Transcript|ENST00000472706|processed_transcript||2/4|ENST00000472706.1:n.209-26580del|||||||||-1||HGNC|20066|||||,-|upstream_gene_variant|MODIFIER|RP11-479F13.1|ENSG00000271146|Transcript|ENST00000605372|processed_pseudogene|||||||||||1594|1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.357445;gno_non_neuro_af_nfe=0.346886;gno_non_neuro_nhomalt_all=139;gno_non_neuro_nhomalt_nfe=80;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:17,0:19:50:0,50,332 0/1:5,6:13:83:83,0,95 0/0:9,0:10:26:0,26,169 0/1:8,9:17:99:123,0,111 0/1:5,6:12:86:87,0,86 0/0:16,0:16:48:0,48,461 1/0:1,6:15:99:303,221,297 0/0:10,0:11:3:0,30,280 0/1:4,4:8:45:48,0,45 0/1:4,3:7:41:41,0,60 0/1:4,1:6:13:13,0,57 -chr2 65103319 rs7589210 T C 3429.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.267;DB;DP=396;ExcessHet=9.0714;FS=6.104;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.35;ReadPosRankSum=-0.821;SOR=0.842;VQSLOD=24;culprit=MQRankSum;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=14.1;gno_non_neuro_af_all=0.556663;gno_non_neuro_af_nfe=0.484578;gno_non_neuro_nhomalt_all=3367;gno_non_neuro_nhomalt_nfe=1561;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:42,0:42:91:0,91,1332 0/1:14,10:24:99:275,0,394 0/0:34,0:34:71:0,71,1074 0/1:20,11:31:99:289,0,572 0/1:15,21:36:99:597,0,414 0/0:36,0:36:99:0,100,1221 0/1:15,13:28:99:368,0,427 0/0:43,0:43:70:0,70,1295 0/1:13,23:36:99:636,0,344 0/1:16,22:38:99:641,0,432 0/1:21,25:46:99:641,0,583 -chr2 65103814 rs6546107 A G 3347.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.192;DB;DP=449;ExcessHet=9.0714;FS=3.177;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=11.16;ReadPosRankSum=-0.024;SOR=0.534;VQSLOD=23.48;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.506841;gno_non_neuro_af_nfe=0.473258;gno_non_neuro_nhomalt_all=2723;gno_non_neuro_nhomalt_nfe=1490;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,99,1371 0/1:19,12:31:99:299,0,568 0/0:33,0:33:90:0,90,1138 0/1:17,12:29:99:310,0,484 0/1:24,20:44:99:538,0,662 0/0:35,0:35:99:0,102,1530 0/1:10,13:23:99:363,0,258 0/0:44,0:44:99:0,103,1410 0/1:37,25:62:99:582,0,1090 0/1:26,26:52:99:647,0,713 0/1:33,26:59:99:626,0,960 -chr2 65103931 rs10639084 G GTTT 4502.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.179;DB;DP=397;ExcessHet=9.0714;FS=2.238;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=19.41;ReadPosRankSum=-0.356;SOR=0.871;VQSLOD=8.92;culprit=MQRankSum;CSQ=TTT|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.509393;gno_non_neuro_af_nfe=0.46758;gno_non_neuro_nhomalt_all=2515;gno_non_neuro_nhomalt_nfe=1338;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:22,0:22:60:0,60,900 0/1:8,10:18:99:371,0,325 0/0:35,0:35:99:0,99,1485 0/1:24,12:36:99:429,0,1023 0/1:18,15:33:99:561,0,743 0/0:33,0:33:99:0,99,1066 0/1:7,16:23:99:643,0,265 0/0:41,0:41:99:0,108,1370 0/1:15,20:35:99:759,0,584 0/1:18,24:42:99:962,0,685 0/1:24,21:45:99:795,0,933 -chr2 65103983 rs6546108 G A 3164.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.904;DB;DP=381;ExcessHet=9.0714;FS=7.072;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.24;ReadPosRankSum=-0.244;SOR=0.843;VQSLOD=24.28;culprit=MQRankSum;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.504025;gno_non_neuro_af_nfe=0.469158;gno_non_neuro_nhomalt_all=2647;gno_non_neuro_nhomalt_nfe=1431;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:33,0:33:75:0,75,1078 0/1:10,13:23:99:383,0,278 0/0:28,0:28:81:0,81,933 0/1:26,13:39:99:315,0,752 0/1:15,16:31:99:453,0,428 0/0:38,0:38:99:0,108,1620 0/1:8,18:26:99:502,0,200 0/0:41,0:41:99:0,108,1370 0/1:21,19:40:99:494,0,600 0/1:14,21:35:99:589,0,382 0/1:28,17:45:99:446,0,782 -chr2 65104485 rs10200233 A G 4388.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.493;DB;DP=473;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.76;ReadPosRankSum=0;SOR=0.705;VQSLOD=23.5;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.52367;gno_non_neuro_af_nfe=0.475941;gno_non_neuro_nhomalt_all=2933;gno_non_neuro_nhomalt_nfe=1508;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,104,1575 0/1:17,23:40:99:669,0,451 0/0:42,0:42:92:0,92,1391 0/1:16,26:42:99:737,0,365 0/1:21,25:46:99:681,0,581 0/0:34,0:34:99:0,99,1162 0/1:25,12:37:99:271,0,708 0/0:36,0:36:99:0,99,1160 0/1:25,28:53:99:673,0,700 0/1:23,20:43:99:460,0,671 0/1:21,37:58:99:915,0,556 -chr2 65106350 rs918197 C T 4206.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.16;DB;DP=462;ExcessHet=9.0714;FS=0.869;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.84;ReadPosRankSum=-0.173;SOR=0.697;VQSLOD=23.74;culprit=MQRankSum;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.527461;gno_non_neuro_af_nfe=0.475917;gno_non_neuro_nhomalt_all=2999;gno_non_neuro_nhomalt_nfe=1513;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,120,1800 0/1:15,22:37:99:613,0,380 0/0:36,0:36:99:0,99,1252 0/1:16,14:30:99:386,0,462 0/1:24,22:46:99:596,0,695 0/0:40,0:40:99:0,100,1275 0/1:19,15:34:99:409,0,548 0/0:35,0:35:99:0,99,1177 0/1:24,32:56:99:944,0,524 0/1:25,14:39:99:370,0,636 0/1:30,32:62:99:906,0,745 -chr2 65106492 rs918196 A G 3868.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.85;DB;DP=446;ExcessHet=9.0714;FS=3.167;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.25;ReadPosRankSum=0.09;SOR=0.883;VQSLOD=23.77;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.528879;gno_non_neuro_af_nfe=0.47651;gno_non_neuro_nhomalt_all=3011;gno_non_neuro_nhomalt_nfe=1513;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,120,1800 0/1:18,12:30:99:326,0,532 0/0:36,0:36:99:0,99,1252 0/1:19,12:31:99:313,0,546 0/1:24,16:40:99:411,0,715 0/0:42,0:42:99:0,100,1395 0/1:16,17:33:99:462,0,457 0/0:30,0:30:81:0,81,1215 0/1:20,25:45:99:709,0,560 0/1:25,29:54:99:834,0,707 0/1:30,29:59:99:831,0,843 -chr2 65106712 rs11396721 T TG 3606.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.845;DB;DP=422;ExcessHet=9.0714;FS=8.562;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.04;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.46;ReadPosRankSum=-0.241;SOR=1.136;VQSLOD=8.78;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.552132;gno_non_neuro_af_nfe=0.482733;gno_non_neuro_nhomalt_all=3298;gno_non_neuro_nhomalt_nfe=1553;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,102,1332 0/1:16,14:30:99:382,0,416 0/0:33,0:33:99:0,99,1107 0/1:15,14:29:99:358,0,390 0/1:21,22:43:99:562,0,538 0/0:37,0:37:99:0,99,1210 0/1:17,23:40:99:609,0,419 0/0:34,0:34:99:0,99,1201 0/1:26,23:49:99:583,0,679 0/1:15,17:32:99:471,0,367 0/1:20,25:45:99:659,0,500 -chr2 65107942 rs6720589 G A 4067.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.59;DB;DP=447;ExcessHet=9.0714;FS=3.057;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.29;ReadPosRankSum=0.115;SOR=0.764;VQSLOD=23.72;culprit=MQRankSum;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.493539;gno_non_neuro_af_nfe=0.469991;gno_non_neuro_nhomalt_all=2570;gno_non_neuro_nhomalt_nfe=1474;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,99,1172 0/1:11,9:20:99:253,0,302 0/0:37,0:37:99:0,99,1340 0/1:22,25:47:99:708,0,613 0/1:24,19:43:99:531,0,685 0/0:31,0:31:93:0,93,1047 0/1:18,22:40:99:624,0,440 0/0:38,0:38:99:0,99,1272 0/1:26,24:50:99:664,0,593 0/1:22,11:33:99:283,0,581 0/1:37,36:73:99:1022,0,926 -chr2 65108615 rs6739118 T C 4243.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.861;DB;DP=479;ExcessHet=9.0714;FS=8.259;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.78;ReadPosRankSum=0.189;SOR=0.421;VQSLOD=23.99;culprit=MQRankSum;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.523677;gno_non_neuro_af_nfe=0.476583;gno_non_neuro_nhomalt_all=2941;gno_non_neuro_nhomalt_nfe=1515;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,99,1071 0/1:13,18:31:99:532,0,339 0/0:37,0:37:99:0,99,1201 0/1:30,21:51:99:567,0,870 0/1:16,16:32:99:450,0,460 0/0:39,0:39:99:0,99,1485 0/1:18,15:33:99:372,0,502 0/0:35,0:35:99:0,100,1196 0/1:25,22:47:99:513,0,728 0/1:30,33:63:99:773,0,844 0/1:33,42:75:99:1054,0,922 -chr2 65109039 rs1995829 A G 3936.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.843;DB;DP=473;ExcessHet=9.0714;FS=2.363;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.96;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12;ReadPosRankSum=0.182;SOR=0.638;VQSLOD=8.81;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.523857;gno_non_neuro_af_nfe=0.4766;gno_non_neuro_nhomalt_all=2945;gno_non_neuro_nhomalt_nfe=1516;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:33,0:33:99:0,99,1077 0/1:23,22:45:99:629,0,664 0/0:37,0:37:99:0,99,1201 0/1:30,14:44:99:344,0,900 0/1:14,17:31:99:488,0,392 0/0:39,0:39:99:0,101,1332 0/1:15,21:36:99:622,0,388 0/0:33,0:33:93:0,93,1395 0/1:31,20:51:99:451,0,904 0/1:26,25:51:99:550,0,741 0/1:34,36:70:99:870,0,971 -chr2 65388081 rs200658875 TA T 3087.91 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.396;DB;DP=291;ExcessHet=9.0714;FS=15.397;InbreedingCoeff=-0.6923;MLEAC=9;MLEAF=0.409;MQ=59.33;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=19.79;ReadPosRankSum=0.534;SOR=1.689;VQSLOD=6.12;culprit=MQRankSum;CSQ=-|downstream_gene_variant|MODIFIER|SNORA74|ENSG00000272025|Transcript|ENST00000607595|snoRNA|||||||||||2088|1||RFAM||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.505715;gno_non_neuro_af_nfe=0.526476;gno_non_neuro_nhomalt_all=2246;gno_non_neuro_nhomalt_nfe=1563;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:21,0:21:0:.:.:0,0,485:. 0|1:7,13:20:99:0|1:65388073_T_A:525,0,552:65388073 0/0:44,0:44:0:.:.:0,0,798:. 0|1:12,9:21:99:0|1:65388073_T_A:311,0,589:65388073 0|1:13,15:28:99:0|1:65388073_T_A:588,0,695:65388073 0/0:30,0:30:0:.:.:0,0,449:. 0|1:4,9:13:99:0|1:65388073_T_A:366,0,147:65388073 0/0:30,0:30:0:.:.:0,0,450:. 0/1:14,14:28:99:.:.:336,0,323:. 0/1:7,10:17:99:.:.:249,0,146:. 0|1:12,17:29:99:0|1:65388073_T_A:712,0,677:65388073 -chr2 65525953 rs34148687 A ATT 2704.68 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.095;DB;DP=280;ExcessHet=4.4261;FS=1.965;InbreedingCoeff=-0.2222;MLEAC=7;MLEAF=0.318;MQ=56.39;MQRankSum=0;QD=15.91;ReadPosRankSum=-0.183;SOR=1.019;VQSLOD=-0.3518;culprit=MQRankSum;CSQ=TT|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.251169;gno_non_neuro_af_nfe=0.27406;gno_non_neuro_nhomalt_all=427;gno_non_neuro_nhomalt_nfe=318;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:12,0:22:99:140,176,388 0/1:0,6:11:43:260,70,43 0/0:9,0:19:99:148,175,334 0/1:1,9:17:89:345,92,89 0/1:0,7:12:67:299,91,67 0/0:11,0:20:99:115,148,342 0/1:1,9:18:99:369,130,119 0/0:0,0:30:89:662,662,662 0/1:0,3:7:79:176,79,159 0/1:0,1:3:11:62,35,32 0/1:4,7:11:90:131,0,90 -chr2 67234368 rs11337895 TA T 901.48 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.645;DB;DP=230;ExcessHet=9.0714;FS=3.637;InbreedingCoeff=-0.5169;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=7.84;ReadPosRankSum=-0.566;SOR=0.397;VQSLOD=7.87;culprit=MQRankSum;CSQ=-|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.538314;gno_non_neuro_af_nfe=0.539987;gno_non_neuro_nhomalt_all=761;gno_non_neuro_nhomalt_nfe=470;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:18,0:18:40:.:.:0,40,577:. 0/1:6,11:17:89:.:.:219,0,89:. 0/0:10,0:10:30:.:.:0,30,338:. 0/1:8,13:21:99:.:.:255,0,121:. 0/1:8,5:13:83:.:.:83,0,149:. 0|0:13,0:13:39:0|1:67234368_T_TAAAAAA:0,39,574:67234368 0/1:5,2:7:28:.:.:28,0,96:. 0/0:30,0:30:0:.:.:0,0,614:. 0/1:9,9:19:99:.:.:167,0,155:. 0/1:9,8:17:99:.:.:137,0,149:. 0/1:18,4:22:26:.:.:26,0,533:. -chr2 69028241 rs138417826 T TA 3489.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.852;DB;DP=456;ExcessHet=9.0714;FS=4.856;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.04;MQRankSum=0;QD=12.69;ReadPosRankSum=-0.452;SOR=0.47;VQSLOD=8.44;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000295381|protein_coding||4/10|ENST00000295381.3:c.467-6158dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409030|protein_coding||3/9|ENST00000409030.3:c.446-6158dup|||||||||1||HGNC|28951||CCDS46312.1|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409202|protein_coding||4/10|ENST00000409202.3:c.467-6155dup|||||||||1||HGNC|28951|YES|CCDS33214.2|||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000409220|protein_coding||3/9|ENST00000409220.1:c.446-6155dup|||||||||1||HGNC|28951||CCDS54364.1|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000456116|processed_transcript||3/4|ENST00000456116.2:n.685-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000463483|nonsense_mediated_decay||5/7|ENST00000463483.1:c.389-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000467265|protein_coding||3/9|ENST00000467265.1:c.350-6158dup|||||||||1||HGNC|28951||CCDS54363.1|||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000473986|nonsense_mediated_decay||4/7|ENST00000473986.1:c.*292-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000485700|processed_transcript||4/4|ENST00000485700.1:n.634-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000488795|nonsense_mediated_decay||2/4|ENST00000488795.1:c.262-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000497079|protein_coding||3/7|ENST00000497079.1:c.446-6155dup|||||||||1||HGNC|28951|||||,A|intron_variant|MODIFIER|ARHGAP25|ENSG00000163219|Transcript|ENST00000544262|protein_coding||4/6|ENST00000544262.1:c.389-6155dup|||||||||1||HGNC|28951|||||;cadd_phred=-1;gno_non_neuro_af_all=0.474334;gno_non_neuro_af_nfe=0.504923;gno_non_neuro_nhomalt_all=2296;gno_non_neuro_nhomalt_nfe=1651;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1261 0/1:10,26:36:99:635,0,173 0/0:39,0:39:99:0,103,1297 0/1:18,20:38:99:457,0,402 0/1:15,18:33:99:415,0,330 0/0:40,0:40:99:0,99,1485 0/1:15,11:26:99:236,0,353 0/0:36,0:36:99:0,100,1266 0/1:21,28:49:99:672,0,451 0/1:19,17:36:99:378,0,435 0/1:26,31:57:99:714,0,574 -chr2 71706563 rs13007337 G C 2232.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.192;DB;DP=390;ExcessHet=9.0714;FS=8.279;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=9.19;ReadPosRankSum=-0.344;SOR=1;VQSLOD=24.29;culprit=MQRankSum;CSQ=C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000258104|protein_coding||1/54|ENST00000258104.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS1918.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000394120|protein_coding||1/54|ENST00000394120.2:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46331.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409366|protein_coding||1/55|ENST00000409366.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46330.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409582|protein_coding||1/55|ENST00000409582.3:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46324.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409651|protein_coding||1/55|ENST00000409651.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46327.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409744|protein_coding||1/54|ENST00000409744.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46332.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000409762|protein_coding||1/54|ENST00000409762.1:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46325.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410020|protein_coding||1/55|ENST00000410020.3:c.92-1450G>C|||||||||1||HGNC|3097|YES|CCDS46328.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000410041|protein_coding||1/54|ENST00000410041.1:c.92-1450G>C|||||||||1||HGNC|3097||CCDS46329.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000413539|protein_coding||1/55|ENST00000413539.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46323.1|||,C|intron_variant|MODIFIER|DYSF|ENSG00000135636|Transcript|ENST00000429174|protein_coding||1/55|ENST00000429174.2:c.89-1450G>C|||||||||1||HGNC|3097||CCDS46326.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.340463;gno_non_neuro_af_nfe=0.411795;gno_non_neuro_nhomalt_all=1286;gno_non_neuro_nhomalt_nfe=1098;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:31,0:31:90:0,90,1350 0/1:14,12:26:99:329,0,352 0/0:25,0:25:72:0,72,849 0/1:19,12:31:99:313,0,567 0/1:24,14:38:99:372,0,717 0/0:34,0:34:99:0,99,1485 0/1:20,9:29:99:201,0,599 0/0:38,0:38:99:0,101,1250 0/1:18,15:33:99:327,0,527 0/1:27,16:43:99:327,0,781 0/1:26,17:43:99:381,0,752 -chr2 114352135 rs3982679 G A 665.14 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.216;DB;DP=554;ExcessHet=9.0714;FS=49.345;InbreedingCoeff=-0.4741;MLEAC=7;MLEAF=0.318;MQ=42.7;MQRankSum=-3.311;QD=1.79;ReadPosRankSum=-0.866;SOR=4.068;VQSLOD=-32.31;culprit=SOR;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000326632|transcribed_unprocessed_pseudogene||2/10|ENST00000326632.7:n.205-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000437401|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000453662|transcribed_unprocessed_pseudogene||1/9|ENST00000453662.2:n.155-505G>A|||||||||1||HGNC|33145|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000457993|unprocessed_pseudogene|||||||||||4478|-1||HGNC|37103|||||,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|Transcript|ENST00000535848|unprocessed_pseudogene|||||||||||4471|-1||HGNC|37103|YES||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|Transcript|ENST00000538033|retained_intron|1/7||ENST00000538033.2:n.383G>A||383/2800|||||||1||HGNC|33145|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.092277;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0950659;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;genic;highest_impact_order=39;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:46,0:46:79:0,79,1390 0/1:33,9:42:99:139,0,965 0/0:34,0:34:43:0,43,1053 0/1:51,14:65:99:207,0,1544 0/1:43,7:50:63:63,0,1392 0/0:43,3:46:47:0,47,1416 0/1:47,12:59:99:170,0,1383 0/0:49,5:54:8:0,8,1534 0/1:42,6:48:12:12,0,1239 0/1:39,8:47:63:63,0,1060 0/1:52,8:60:28:28,0,1503 -chr7 628664 rs73254203 A G 533.56 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-1.067;DB;DP=545;ExcessHet=9.0714;FS=0.653;InbreedingCoeff=-0.5133;MLEAC=7;MLEAF=0.318;MQ=54.65;MQRankSum=-4.686;QD=2.21;ReadPosRankSum=1.18;SOR=0.58;VQSLOD=-3.475;culprit=MQ;CSQ=G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000360274|protein_coding||7/10|ENST00000360274.4:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000400758|protein_coding||2/5|ENST00000400758.2:c.291-4459T>C|||||||||-1|cds_start_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000403562|protein_coding||7/10|ENST00000403562.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000406797|protein_coding||7/10|ENST00000406797.1:c.709-4459T>C|||||||||-1||HGNC|9390|YES|CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000430040|protein_coding||7/8|ENST00000430040.1:c.709-4459T>C|||||||||-1|cds_end_NF|HGNC|9390|||||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000537384|protein_coding||7/10|ENST00000537384.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||,G|intron_variant|MODIFIER|PRKAR1B|ENSG00000188191|Transcript|ENST00000544935|protein_coding||7/10|ENST00000544935.1:c.709-4459T>C|||||||||-1||HGNC|9390||CCDS34579.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.185854;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.188696;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:33,0:33:0:.:.:0,0,788:. 0|1:19,2:21:1:0|1:628664_A_G:1,0,739:628664 0/0:26,0:26:8:.:.:0,8,673:. 0|1:13,2:15:10:0|1:628664_A_G:10,0,442:628664 0|1:38,5:43:70:0|1:628664_A_G:70,0,1523:628664 0/0:27,0:27:12:.:.:0,12,759:. 0|1:11,1:12:6:0|1:628664_A_G:6,0,403:628664 0/0:44,0:44:0:.:.:0,0,1002:. 0|1:46,12:58:99:0|1:628664_A_G:149,0,2480:628664 0|1:28,6:34:99:0|1:628664_A_G:129,0,2666:628664 0|1:60,10:70:99:0|1:628664_A_G:177,0,3575:628664 -chr7 143492092 . C T 975.5 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=1.06;DP=299;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.5172;MLEAC=7;MLEAF=0.318;MQ=39.44;MQRankSum=0;QD=5.19;ReadPosRankSum=0.319;SOR=0.346;VQSLOD=-4.537;culprit=MQ;CSQ=T|upstream_gene_variant|MODIFIER|RP11-307I2.1|ENSG00000232145|Transcript|ENST00000421443|processed_pseudogene|||||||||||1296|1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000422705|transcribed_unprocessed_pseudogene||1/5|ENST00000422705.2:n.66+41641G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000427403|transcribed_unprocessed_pseudogene||2/6|ENST00000427403.1:n.692+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000450076|transcribed_unprocessed_pseudogene||2/6|ENST00000450076.1:n.706+38248G>A|||||||||-1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM115D|ENSG00000159860|Transcript|ENST00000456362|unprocessed_pseudogene||1/6|ENST00000456362.1:n.133-14991C>T|||||||||1||HGNC|33603|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-61L23.2|ENSG00000253882|Transcript|ENST00000491047|processed_transcript||3/4|ENST00000491047.1:n.304+16549G>A|||||||||-1||Clone_based_vega_gene||||||;cadd_phred=-1;gno_non_neuro_af_all=0.0307973;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0267106;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:22,0:22:66:0,66,735 0/1:19,5:24:99:102,0,578 0/0:28,0:28:0:0,0,735 0/1:29,6:35:99:104,0,868 0/1:24,6:30:99:119,0,706 0/0:31,0:31:93:0,93,1068 0/1:14,4:18:85:85,0,382 0/0:30,0:30:87:0,87,1305 0/1:15,14:29:99:390,0,278 0/1:20,4:24:64:64,0,431 0/1:22,6:28:99:125,0,469 -chr7 143897347 rs147865002 A G 963.51 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=309;ExcessHet=9.0714;FS=85.285;InbreedingCoeff=-0.5174;MLEAC=7;MLEAF=0.318;MQ=33.37;MQRankSum=1.79;QD=4.24;ReadPosRankSum=-0.238;SOR=6.827;VQSLOD=-97.48;culprit=SOR;CSQ=G|upstream_gene_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000378115|protein_coding|||||||||||4599|-1||HGNC|33846|YES|CCDS34770.1|||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.381+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense|2/6||ENST00000464929.1:n.432A>G||432/819|||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense|2/4||ENST00000474656.1:n.428A>G||428/773|||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.170+4197A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.183+4553A>G|||||||||1||Clone_based_vega_gene||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense|2/5||ENST00000498693.1:n.366A>G||366/856|||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-11859T>C|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.26168;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.250156;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=55;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=37;gno_non_neuro_nhomalt_nfe_filter;genic;highest_impact_order=39;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1485 0/1:26,5:31:78:78,0,758 0/0:20,0:20:0:0,0,546 0/1:22,6:28:99:118,0,633 0/1:21,6:27:99:124,0,619 0/0:14,0:14:42:0,42,477 0/1:20,9:29:99:226,0,569 0/0:10,0:10:30:0,30,327 0/1:30,7:37:99:123,0,868 0/1:25,5:30:74:74,0,717 0/1:34,11:45:99:234,0,958 -chr7 143901937 . C T 1396.5 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.501;DP=670;ExcessHet=9.0714;FS=4.325;InbreedingCoeff=-0.5172;MLEAC=7;MLEAF=0.318;MQ=27.51;MQRankSum=0.158;QD=3.03;ReadPosRankSum=0.108;SOR=0.991;VQSLOD=-10.21;culprit=MQ;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2846|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2848|1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2849C>T|||||||||1||Clone_based_vega_gene||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2849C>T|||||||||1||Clone_based_vega_gene||YES||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16449G>A|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.134101;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.103901;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=9;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,99,1172 0/1:51,12:63:99:172,0,1373 0/0:99,0:99:0:0,0,2745 0/1:71,14:85:99:167,0,1970 0/1:86,12:98:73:73,0,2339 0/0:38,0:38:99:0,102,1361 0/1:34,14:48:99:289,0,938 0/0:38,0:38:99:0,100,1232 0/1:47,8:55:89:89,0,1303 0/1:41,10:51:99:157,0,1140 0/1:40,21:61:99:463,0,1066 -chr7 143901963 rs199990667 G A 1765.37 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=1.5;DB;DP=878;ExcessHet=9.0714;FS=1.528;InbreedingCoeff=-0.4643;MLEAC=7;MLEAF=0.318;MQ=27.67;MQRankSum=0.017;QD=2.73;ReadPosRankSum=0.773;SOR=0.67;VQSLOD=-10.09;culprit=MQ;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||2820|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||2822|1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-2823G>A|||||||||1||Clone_based_vega_gene||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-2823G>A|||||||||1||Clone_based_vega_gene||YES||||,A|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-16475C>T|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.182612;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.148653;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=11;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,99,1172 0/1:66,14:80:99:191,0,1971 0/0:112,10:122:44:0,44,3264 0/1:86,15:101:99:173,0,2550 0/1:104,12:116:16:16,0,3073 0/0:38,0:38:99:0,102,1361 0/1:43,19:62:99:382,0,1249 0/0:38,0:38:99:0,100,1232 0/1:74,12:86:99:123,0,2013 0/1:79,12:91:72:72,0,2228 0/1:72,38:110:99:826,0,2017 -chr7 143904241 rs149376936 A G 1691.5 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.018;DB;DP=701;ExcessHet=9.0714;FS=11.359;InbreedingCoeff=-0.5172;MLEAC=7;MLEAF=0.318;MQ=32.63;MQRankSum=-0.299;QD=3.25;ReadPosRankSum=-1.483;SOR=1.497;VQSLOD=-9.891;culprit=MQ;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000460955|antisense||1/2|ENST00000460955.1:n.382-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000464929|antisense||2/5|ENST00000464929.1:n.456-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000474656|antisense||2/3|ENST00000474656.1:n.452-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000477797|antisense|||||||||||542|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000480074|antisense||1/2|ENST00000480074.1:n.171-545A>G|||||||||1||Clone_based_vega_gene||||||,G|upstream_gene_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000489077|antisense|||||||||||544|1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000493248|antisense||1/4|ENST00000493248.1:n.184-545A>G|||||||||1||Clone_based_vega_gene||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-545C24.1|ENSG00000244198|Transcript|ENST00000498693|antisense||2/4|ENST00000498693.1:n.390-545A>G|||||||||1||Clone_based_vega_gene||YES||||,G|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-12-18753T>C|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.274984;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.262682;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=1;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=1;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,99,1232 0/1:53,16:69:99:287,0,1475 0/0:74,0:74:0:0,0,1977 0/1:49,8:57:80:80,0,1368 0/1:69,15:84:99:227,0,1857 0/0:34,0:34:99:0,99,1182 0/1:27,15:42:99:331,0,740 0/0:34,0:34:99:0,102,1132 0/1:74,21:95:99:388,0,2021 0/1:58,16:74:99:273,0,1627 0/1:87,13:100:99:119,0,2434 -chr7 143989050 rs200834183 C T 945.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=282;ExcessHet=9.0714;FS=7.071;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=26.71;MQRankSum=0;QD=4.95;ReadPosRankSum=-0.532;SOR=0.952;VQSLOD=-10.45;culprit=MQ;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2161G>A|||||||||-1||HGNC|38086|YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40347G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19634G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40347G>A|||||||||-1||HGNC|49168|||||,T|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2523|1||HGNC|8236|||||,T|upstream_gene_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000483587|unprocessed_pseudogene|||||||||||4991|-1||HGNC|38086|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37261G>A|||||||||-1||HGNC|49168|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39465G>A|||||||||-1||HGNC|49168|||||,T|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2161G>A|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.300719;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.280411;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=8;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=6;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:32,0:32:96:0,96,1062 0/1:21,5:26:75:75,0,582 0/0:25,0:25:50:0,50,810 0/1:11,3:14:52:52,0,290 0/1:20,9:29:99:186,0,487 0/0:16,0:16:48:0,48,556 0/1:9,7:16:99:165,0,220 0/0:17,0:17:51:0,51,591 0/1:22,8:30:99:148,0,564 0/1:25,10:35:99:187,0,640 0/1:31,10:41:99:150,0,780 -chr7 143989124 rs201464581 T C 1771.5 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-2.573;DB;DP=437;ExcessHet=9.0714;FS=13.386;InbreedingCoeff=-0.5172;MLEAC=7;MLEAF=0.318;MQ=25.57;MQRankSum=0;QD=5.87;ReadPosRankSum=-0.174;SOR=1.348;VQSLOD=-14;culprit=MQ;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|ARHGEF34P|ENSG00000204959|Transcript|ENST00000378112|unprocessed_pseudogene||1/11|ENST00000378112.1:n.46+2087A>G|||||||||-1||HGNC|38086|YES||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000461843|antisense||1/1|ENST00000461843.1:n.113-40421A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000463561|antisense||5/5|ENST00000463561.1:n.578+19560A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000476560|antisense||1/2|ENST00000476560.1:n.158-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000478806|antisense||1/1|ENST00000478806.1:n.371-40421A>G|||||||||-1||HGNC|49168|||||,C|upstream_gene_variant|MODIFIER|OR2A9P|ENSG00000228960|Transcript|ENST00000479102|processed_transcript|||||||||||2449|1||HGNC|8236|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000487102|antisense||2/2|ENST00000487102.1:n.161-37335A>G|||||||||-1||HGNC|49168|||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|OR2A1-AS1|ENSG00000244479|Transcript|ENST00000489488|antisense||1/1|ENST00000489488.1:n.264-39539A>G|||||||||-1||HGNC|49168|||||,C|intron_variant|MODIFIER|ARHGEF35|ENSG00000213214|Transcript|ENST00000543357|protein_coding||1/1|ENST00000543357.1:c.-13+2087A>G|||||||||-1||HGNC|33846||CCDS34770.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.31982;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.305004;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=4;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=4;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,99,1232 0/1:22,11:33:99:228,0,569 0/0:44,0:44:0:0,0,1252 0/1:30,9:39:99:151,0,781 0/1:34,14:48:99:258,0,868 0/0:25,0:25:72:0,72,863 0/1:14,12:26:99:279,0,338 0/0:30,0:30:90:0,90,1033 0/1:36,15:51:99:258,0,918 0/1:39,15:54:99:240,0,974 0/1:32,19:51:99:371,0,799 -chr7 144659042 rs57146390 TATACAC T 997.48 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=313;ExcessHet=9.0714;FS=6.166;InbreedingCoeff=-0.5298;MLEAC=7;MLEAF=0.318;MQ=60.14;MQRankSum=0;QD=7.61;ReadPosRankSum=0.794;SOR=0.752;VQSLOD=7.17;culprit=MQRankSum;CSQ=-|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.0591229;gno_non_neuro_af_nfe=0.0532034;gno_non_neuro_nhomalt_all=13;gno_non_neuro_nhomalt_nfe=5;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,750 0/1:14,7:21:99:152,0,596 0/0:12,1:13:7:0,7,495 0/1:14,4:18:75:75,0,576 0/1:15,9:24:99:207,0,718 0/0:28,0:28:0:0,0,432 0/1:7,12:19:99:306,0,323 0/0:17,0:17:51:0,51,765 0/1:9,2:12:13:13,0,536 0/1:5,6:11:99:156,0,214 0/1:21,6:28:99:101,0,1004 -chr7 146603134 rs4295575 G A 5086.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.052;DB;DP=478;ExcessHet=9.0714;FS=5.008;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=53.32;MQRankSum=0.189;NEGATIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=0.593;SOR=0.489;VQSLOD=-1.811;culprit=MQ;CSQ=A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.402+66138G>A|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0395233;gno_non_neuro_af_nfe=0.0491249;gno_non_neuro_nhomalt_all=12;gno_non_neuro_nhomalt_nfe=10;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,102,1381 0/1:12,18:30:99:525,0,327 0/0:32,0:32:96:0,96,1042 0/1:26,21:47:99:544,0,723 0/1:19,37:56:99:1058,0,492 0/0:43,0:43:99:0,114,1510 0/1:23,19:42:99:494,0,653 0/0:34,0:34:99:0,99,1111 0/1:26,26:52:99:732,0,627 0/1:15,26:41:99:768,0,338 0/1:27,35:62:99:983,0,597 -chr7 146655898 . C G 4675.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.18;DP=448;ExcessHet=9.0714;FS=1.828;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=14.43;ReadPosRankSum=0.683;SOR=0.819;VQSLOD=21.97;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||3/23|ENST00000361727.3:c.403-85101C>G|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:28,0:28:78:0,78,1029 0/1:11,16:27:99:465,0,266 0/0:40,0:40:99:0,104,1281 0/1:15,21:36:99:622,0,388 0/1:23,19:42:99:535,0,618 0/0:28,0:28:81:0,81,953 0/1:20,16:36:99:423,0,567 0/0:26,0:26:78:0,78,904 0/1:23,30:53:99:884,0,614 0/1:25,34:59:99:970,0,672 0/1:42,29:71:99:794,0,1201 -chr7 146778675 rs5888235;rs5888236;rs72004618 T TTG 3161.52 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.231;DB;DP=332;ExcessHet=11.8014;FS=5.311;InbreedingCoeff=-0.5714;MLEAC=7;MLEAF=0.318;MQ=59.84;MQRankSum=0;QD=17.37;ReadPosRankSum=-0.222;SOR=0.642;VQSLOD=6.77;culprit=MQRankSum;CSQ=TG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-26520_551-26519dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,TG|non_coding_transcript_exon_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense|4/4||ENST00000434887.1:n.1494_1495dup||1495-1496/2145|||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.0743969;gno_non_neuro_af_nfe=0.051922;gno_non_neuro_nhomalt_all=83;gno_non_neuro_nhomalt_nfe=14;genic;highest_impact_order=39;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:17,0:29:99:.:.:454,505,1242:. 0|1:8,4:12:80:0|1:146778675_T_TTG:80,0,182:146778675 0/0:12,0:22:99:.:.:385,421,925:. 0/1:6,9:15:99:.:.:204,0,115:. 0/1:6,11:17:99:.:.:246,0,113:. 0/0:10,0:22:99:.:.:459,489,916:. 1/0:0,4:12:99:.:.:288,216,321:. 0/0:8,0:21:99:.:.:422,381,625:. 0/1:5,3:8:56:.:.:56,0,112:. 0/1:0,3:12:80:.:.:433,362,354:. 1/0:2,5:12:81:.:.:177,83,210:. -chr7 146790164 rs10596701;rs10603504;rs71165068 C CAT 10890.1 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=452;ExcessHet=3.6798;FS=8.604;InbreedingCoeff=-0.1579;MLEAC=7;MLEAF=0.318;MQ=59.87;MQRankSum=0;QD=29.2;ReadPosRankSum=0.461;SOR=0.459;VQSLOD=5.58;culprit=MQRankSum;CSQ=AT|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||4/23|ENST00000361727.3:c.551-15056_551-15055dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||,AT|intron_variant&non_coding_transcript_variant|MODIFIER|AC006004.1|ENSG00000236795|Transcript|ENST00000434887|antisense||1/3|ENST00000434887.1:n.178+4358_178+4359dup|||||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.0176655;gno_non_neuro_af_nfe=0.0213255;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_nfe=1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:8,0:24:99:504,528,791 0/1:13,13:26:99:381,0,355 0/0:0,0:36:99:1294,1294,1294 0/1:0,18:27:99:851,283,266 0/1:0,25:49:99:1584,851,918 0/0:0,0:26:78:948,948,948 0/1:16,13:29:99:397,0,475 0/0:1,0:31:58:1059,1062,1095 0/1:1,18:41:99:1268,739,836 0/1:1,15:39:99:1190,761,883 0/1:1,25:45:99:1413,631,708 -chr7 146834965 rs57215903;rs5888238 G GTAGA 5515.04 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.126;DB;DP=475;ExcessHet=9.3779;FS=8.071;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.28;MQRankSum=0.905;QD=22.79;ReadPosRankSum=0.714;SOR=0.948;VQSLOD=1.87;culprit=FS;CSQ=TAGA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1348+5404_1348+5407dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.223366;gno_non_neuro_af_nfe=0.21519;gno_non_neuro_nhomalt_all=457;gno_non_neuro_nhomalt_nfe=274;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0|0:11,0:27:99:0|1:146834965_G_GTAGATAGA:714,749,1212:146834965 0/1:0,16:25:99:.:.:1194,388,329:. 0/0:34,0:34:96:.:.:0,96,1440:. 0/1:12,16:28:99:.:.:624,0,526:. 0/1:9,12:21:99:.:.:476,0,409:. 0/0:37,0:37:99:.:.:0,100,1205:. 0/1:11,16:27:99:.:.:616,0,473:. 0/0:11,0:23:99:.:.:451,484,987:. 0|1:23,9:32:99:0|1:146834965_G_GTAGA:304,0,927:146834965 0|1:15,16:31:99:0|1:146834965_G_GTAGA:640,0,582:146834965 0|1:15,13:28:99:0|1:146834965_G_GTAGA:538,0,578:146834965 -chr7 146944250 . A G 4499.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.356;DP=450;ExcessHet=9.0714;FS=5.792;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=14.15;ReadPosRankSum=0.214;SOR=0.52;VQSLOD=22.12;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-52983A>G|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:31,0:31:93:0,93,1017 0/1:22,20:42:99:569,0,593 0/0:32,0:32:90:0,90,1350 0/1:16,27:43:99:750,0,408 0/1:16,21:37:99:584,0,435 0/0:37,0:37:99:0,102,1266 0/1:14,21:35:99:605,0,381 0/0:30,0:30:90:0,90,1043 0/1:16,25:41:99:736,0,422 0/1:29,21:50:99:555,0,858 0/1:43,27:70:99:718,0,1282 -chr7 146983589 rs185313161 C T 5317.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=2.36;DB;DP=508;ExcessHet=9.0714;FS=4.61;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=0.217;SOR=0.552;VQSLOD=23.44;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||8/23|ENST00000361727.3:c.1349-13644C>T|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0140439;gno_non_neuro_af_nfe=0.0185213;gno_non_neuro_nhomalt_all=4;gno_non_neuro_nhomalt_nfe=4;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,105,1256 0/1:20,17:37:99:448,0,436 0/0:37,0:37:99:0,99,1230 0/1:14,24:38:99:720,0,342 0/1:25,19:44:99:483,0,727 0/0:35,0:35:99:0,102,1076 0/1:10,13:23:99:383,0,268 0/0:34,0:34:99:0,102,1121 0/1:29,28:57:99:778,0,662 0/1:37,43:80:99:1244,0,824 0/1:39,46:85:99:1279,0,835 -chr7 147053066 . C T 3979.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DP=462;ExcessHet=9.0714;FS=0.839;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.94;MQRankSum=0;QD=12.1;ReadPosRankSum=0.836;SOR=0.766;VQSLOD=6.9;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-39635C>T|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=4.705e-05;gno_non_neuro_af_nfe=0;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_nfe=0;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1307 0/1:19,16:35:99:442,0,496 0/0:36,0:36:99:0,102,1195 0/1:32,24:56:99:646,0,879 0/1:21,31:52:99:901,0,563 0/0:37,0:37:99:0,111,1246 0/1:11,15:26:99:444,0,279 0/0:23,0:23:60:0,60,820 0/1:26,12:38:99:303,0,789 0/1:35,24:59:99:646,0,1028 0/1:39,24:63:99:615,0,1165 -chr7 147063869 . GCACGCA G 4498.92 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=0.785;DP=404;ExcessHet=6.4503;FS=21.408;InbreedingCoeff=-0.3167;MLEAC=7;MLEAF=0.318;MQ=60.48;MQRankSum=1.34;NEGATIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=-0.235;SOR=0.848;VQSLOD=-0.7725;culprit=MQ;CSQ=-|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-28828_1499-28823del|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0303613;gno_non_neuro_af_nfe=0.0327977;gno_non_neuro_nhomalt_all=9;gno_non_neuro_nhomalt_nfe=6;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:34,0:34:67:.:.:0,67,1052:. 0/1:15,17:32:99:.:.:638,0,946:. 0/0:37,0:37:27:.:.:0,27,1028:. 0|1:19,11:30:99:0|1:147063869_GCACGCA_G:383,0,744:147063869 0/1:15,22:37:99:.:.:847,0,543:. 0/0:33,0:33:30:.:.:0,30,968:. 0|1:11,14:25:99:0|1:147063869_GCACGCA_G:533,0,399:147063869 0|0:12,0:27:99:0|1:147063868_TGCAC_T:561,598,1102:147063868 0/1:18,26:44:99:.:.:965,0,1085:. 0/1:27,20:47:99:.:.:695,0,1023:. 1/0:0,13:31:99:.:.:1776,591,466:. -chr7 147067882 rs62482227 G T 5110.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.49;DB;DP=499;ExcessHet=9.0714;FS=1.241;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.04;ReadPosRankSum=-0.477;SOR=0.785;VQSLOD=23.37;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||9/23|ENST00000361727.3:c.1499-24819G>T|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0155809;gno_non_neuro_af_nfe=0.0210874;gno_non_neuro_nhomalt_all=6;gno_non_neuro_nhomalt_nfe=6;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,102,1530 0/1:12,25:37:99:732,0,266 0/0:39,0:39:99:0,102,1326 0/1:27,23:50:99:604,0,712 0/1:20,23:43:99:654,0,565 0/0:20,0:20:54:0,54,810 0/1:29,19:48:99:516,0,821 0/0:36,0:36:99:0,99,1285 0/1:30,29:59:99:825,0,845 0/1:27,28:55:99:797,0,763 0/1:37,35:72:99:1000,0,1070 -chr7 147118677 rs10696030;rs145095088;rs55983110 C CTGTGTG 14210.2 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=481;ExcessHet=3.2222;FS=3.536;InbreedingCoeff=-0.1;MLEAC=7;MLEAF=0.318;MQ=60.13;MQRankSum=0;QD=28.73;ReadPosRankSum=-0.114;SOR=0.891;VQSLOD=8.31;culprit=MQRankSum;CSQ=TGTGTG|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+25829_1670+25834dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:0,0:30:99:1584,1448,1424 0/1:0,19:37:99:1657,763,698 0/0:0,0:31:99:1557,1447,1424 1/0:0,12:23:99:973,449,408 1/0:0,15:25:99:1079,422,374 0/0:0,0:33:99:1562,1362,1345 1/0:0,9:19:99:932,470,434 0/0:19,0:44:99:885,949,1792 0/1:0,19:38:99:1877,777,691 1/0:0,10:23:99:1236,612,559 0/1:30,24:54:99:904,0,1951 -chr7 147124964 rs62481225 T G 4824.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=472;ExcessHet=9.0714;FS=5.858;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.66;ReadPosRankSum=0.19;SOR=1.007;VQSLOD=23.86;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+32092T>G|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0221218;gno_non_neuro_af_nfe=0.0290963;gno_non_neuro_nhomalt_all=5;gno_non_neuro_nhomalt_nfe=5;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1281 0/1:14,18:32:99:530,0,390 0/0:33,0:33:87:0,87,1305 0/1:23,16:39:99:394,0,683 0/1:14,22:36:99:656,0,368 0/0:37,0:37:93:0,93,1395 0/1:14,27:41:99:750,0,364 0/0:37,0:37:99:0,99,1230 0/1:24,28:52:99:817,0,657 0/1:23,30:53:99:873,0,638 0/1:45,31:76:99:822,0,1315 -chr7 147128097 rs77602642 G A 3528.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.31;DB;DP=424;ExcessHet=9.0714;FS=0.963;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.94;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.57;ReadPosRankSum=1.08;SOR=0.604;VQSLOD=8.18;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1670+35225G>A|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.12109;gno_non_neuro_af_nfe=0.161241;gno_non_neuro_nhomalt_all=180;gno_non_neuro_nhomalt_nfe=163;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,103,1330 0/1:13,12:25:99:331,0,367 0/0:33,0:33:90:0,90,1350 0/1:16,21:37:99:554,0,420 0/1:20,18:38:99:472,0,521 0/0:42,0:42:99:0,114,1324 0/1:17,13:30:99:362,0,480 0/0:36,0:36:99:0,102,1139 0/1:12,26:38:99:761,0,163 0/1:19,20:39:99:539,0,368 0/1:33,20:53:99:527,0,722 -chr7 147145574 rs10635826 G GTA 3805.34 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.329;DB;DP=472;ExcessHet=20.6;FS=11.925;InbreedingCoeff=-0.8333;MLEAC=7;MLEAF=0.318;MQ=60.18;MQRankSum=0;QD=11.09;ReadPosRankSum=0.58;SOR=0.813;VQSLOD=5.5;culprit=MQRankSum;CSQ=TA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-37452_1671-37451insAT|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.216085;gno_non_neuro_af_nfe=0.241488;gno_non_neuro_nhomalt_all=193;gno_non_neuro_nhomalt_nfe=130;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:18,0:29:99:335,414,1270 0/1:19,14:33:99:374,0,534 0/0:21,0:31:99:258,322,1136 0/1:13,13:26:99:361,0,334 0/1:19,16:35:99:437,0,503 0/0:19,0:34:99:460,518,1250 0/1:13,9:22:99:279,0,405 0/0:40,0:40:99:0,102,1530 0/1:18,19:41:99:606,0,732 0/1:22,12:34:99:284,0,715 0/1:43,19:62:99:442,0,1708 -chr7 147157874 rs62482761 T G 5099.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.968;DB;DP=471;ExcessHet=9.0714;FS=0.407;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.84;ReadPosRankSum=0.27;SOR=0.742;VQSLOD=23.52;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-25153T>G|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0148552;gno_non_neuro_af_nfe=0.0195215;gno_non_neuro_nhomalt_all=5;gno_non_neuro_nhomalt_nfe=5;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,99,1306 0/1:16,11:27:99:291,0,473 0/0:38,0:38:99:0,100,1232 0/1:13,23:36:99:691,0,344 0/1:23,21:44:99:557,0,647 0/0:35,0:35:99:0,99,1197 0/1:13,18:31:99:487,0,359 0/0:35,0:35:99:0,99,1167 0/1:25,31:56:99:909,0,699 0/1:26,37:63:99:1087,0,712 0/1:27,38:65:99:1095,0,743 -chr7 147170359 rs79788773 G A 4328.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.03;DB;DP=466;ExcessHet=9.0714;FS=0.402;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.32;ReadPosRankSum=0.547;SOR=0.737;VQSLOD=23.42;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||10/23|ENST00000361727.3:c.1671-12668G>A|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.129082;gno_non_neuro_af_nfe=0.16696;gno_non_neuro_nhomalt_all=204;gno_non_neuro_nhomalt_nfe=185;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,102,1332 0/1:12,15:27:99:417,0,326 0/0:35,0:35:99:0,99,1485 0/1:16,20:36:99:577,0,446 0/1:19,18:37:99:515,0,524 0/0:38,0:38:99:0,99,1416 0/1:18,10:28:99:250,0,501 0/0:29,0:29:84:0,84,978 0/1:36,29:65:99:813,0,935 0/1:25,28:53:99:804,0,579 0/1:44,35:79:99:970,0,1027 -chr7 147183978 rs62481262 T C 3606.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.659;DB;DP=419;ExcessHet=9.0714;FS=4.886;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.59;MQRankSum=0;QD=13.36;ReadPosRankSum=-0.822;SOR=0.468;VQSLOD=4.37;culprit=MQRankSum;CSQ=C|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+845T>C|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.13837;gno_non_neuro_af_nfe=0.175109;gno_non_neuro_nhomalt_all=200;gno_non_neuro_nhomalt_nfe=181;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:31,0:31:84:.:.:0,84,1260:. 0/1:16,13:29:99:.:.:473,0,655:. 0/0:33,0:33:81:.:.:0,81,1215:. 0|1:18,18:36:99:0|1:147183978_T_C:451,0,494:147183978 0|1:11,18:29:99:0|1:147183978_T_C:497,0,295:147183978 0/0:42,0:42:96:.:.:0,96,1440:. 0/1:12,23:35:99:.:.:648,0,313:. 0/0:42,0:42:99:.:.:0,100,1364:. 0/1:26,19:45:99:.:.:667,0,964:. 0/1:32,15:47:99:.:.:300,0,883:. 0/1:30,19:49:99:.:.:588,0,3088:. -chr7 147191560 rs10562874;rs370624966;rs371899542;rs377095658 C CAAAAA 8243.32 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=288;ExcessHet=3.2222;FS=2.68;InbreedingCoeff=-0.1;MLEAC=7;MLEAF=0.318;MQ=60.07;MQRankSum=1.27;QD=35.92;ReadPosRankSum=-0.14;SOR=0.356;VQSLOD=0.871;culprit=QD;CSQ=AAAAA|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+8441_1777+8445dup|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.160172;gno_non_neuro_af_nfe=0.157468;gno_non_neuro_nhomalt_all=287;gno_non_neuro_nhomalt_nfe=172;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:0,0:11:46:719,495,447 0/1:0,4:16:70:787,349,293 0/0:0,0:27:99:1078,1091,1160 1/0:0,3:21:71:882,756,748 1/0:0,10:22:99:911,491,461 0/0:0,0:27:99:1168,1168,1168 1/0:0,6:16:99:655,404,386 0/0:13,0:31:99:617,668,1316 0/1:0,1:4:15:250,103,83 1/0:0,3:22:99:900,790,782 0/1:6,6:12:99:312,0,327 -chr7 147199809 rs60449695 ATG A 2379.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.335;DB;DP=418;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.04;MQRankSum=0;QD=12.39;ReadPosRankSum=0;SOR=0.721;VQSLOD=8.85;culprit=MQRankSum;CSQ=-|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+16700_1777+16701del|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.142121;gno_non_neuro_af_nfe=0.168577;gno_non_neuro_nhomalt_all=201;gno_non_neuro_nhomalt_nfe=165;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:28,0:28:71:0,71,1029 0/1:9,13:22:99:372,0,378 0/0:31,0:31:87:0,87,1305 0/1:14,8:22:99:213,0,522 0/1:10,11:21:99:321,0,387 0/0:34,0:34:96:0,96,1440 0/1:9,16:25:99:483,0,305 0/0:35,0:35:99:0,99,1177 0/1:20,12:32:99:289,0,1073 0/1:19,8:27:99:185,0,691 0/1:24,19:43:99:534,0,657 -chr7 147205999 rs117125375 G A 4605.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.45;DB;DP=479;ExcessHet=9.0714;FS=3.472;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.55;ReadPosRankSum=0.092;SOR=0.76;VQSLOD=23.44;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|CNTNAP2|ENSG00000174469|Transcript|ENST00000361727|protein_coding||11/23|ENST00000361727.3:c.1777+22866G>A|||||||||1||HGNC|13830|YES|CCDS5889.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0210274;gno_non_neuro_af_nfe=0.027027;gno_non_neuro_nhomalt_all=5;gno_non_neuro_nhomalt_nfe=5;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:31,0:31:90:0,90,1350 0/1:18,15:33:99:403,0,481 0/0:39,0:39:99:0,99,1305 0/1:19,14:33:99:387,0,541 0/1:18,23:41:99:676,0,492 0/0:35,0:35:99:0,99,1286 0/1:28,18:46:99:488,0,790 0/0:34,0:34:99:0,99,1162 0/1:27,25:52:99:713,0,632 0/1:20,23:43:99:670,0,435 0/1:47,45:92:99:1286,0,1114 -chr7 152103755 rs62496960 G A 2001.84 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.796;DB;DP=534;ExcessHet=9.0714;FS=12.11;InbreedingCoeff=-0.4567;MLEAC=7;MLEAF=0.318;MQ=55.8;MQRankSum=-5.587;QD=5.87;ReadPosRankSum=2.02;SOR=0.643;VQSLOD=-2.653;culprit=MQ;CSQ=A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000262189|protein_coding||1/58|ENST00000262189.6:c.161+28956C>T|||||||||-1||HGNC|13726|YES|CCDS5931.1|||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000355193|protein_coding||1/59|ENST00000355193.2:c.161+28956C>T|||||||||-1||HGNC|13726|||||,A|intron_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000452749|protein_coding||1/3|ENST00000452749.1:c.161+28956C>T|||||||||-1|cds_end_NF|HGNC|13726|||||,A|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000253088|Transcript|ENST00000517279|misc_RNA|||||||||||3777|1||RFAM||YES||||,A|intron_variant&NMD_transcript_variant|MODIFIER|KMT2C|ENSG00000055609|Transcript|ENST00000558084|nonsense_mediated_decay||1/58|ENST00000558084.1:c.161+28956C>T|||||||||-1||HGNC|13726|||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,102,1227 0/1:25,3:28:35:35,0,745 0/0:39,0:39:83:0,83,1276 0/1:34,8:42:99:107,0,945 0/1:38,6:44:6:6,0,1113 0/0:40,0:40:16:0,16,1132 0/1:35,8:43:90:90,0,1057 0/0:50,0:50:11:0,11,1390 0/1:39,20:59:99:626,0,967 0/1:37,5:42:66:66,0,1018 0/1:46,37:83:99:1089,0,1139 -chr9 45645893 . C A 845.5 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.248;DP=486;ExcessHet=9.0714;FS=39.551;InbreedingCoeff=-0.4675;MLEAC=7;MLEAF=0.318;MQ=37.36;MQRankSum=-1.297;QD=2.68;ReadPosRankSum=1.44;SOR=2.488;VQSLOD=-23.11;culprit=MQ;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.0477956;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0522528;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:54,0:54:99:0,100,1650 0/1:19,4:23:51:51,0,570 0/0:34,0:34:28:0,28,933 0/1:24,4:28:21:21,0,707 0/1:37,5:42:32:32,0,1094 0/0:37,0:37:61:0,61,1035 0/1:28,10:38:99:196,0,778 0/0:42,4:46:18:0,18,1219 0/1:43,15:58:99:272,0,1156 0/1:37,12:49:99:202,0,948 0/1:67,10:77:89:89,0,1888 -chr9 69791969 rs199990756 G C 392.27 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.67;DB;DP=571;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4585;MLEAC=7;MLEAF=0.318;MQ=31.18;MQRankSum=-1.009;QD=1.12;ReadPosRankSum=0.097;SOR=0.65;VQSLOD=-8.379;culprit=MQ;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.12686;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.146961;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:67,0:67:62:0,62,1890 0/1:37,9:46:84:84,0,1015 0/0:57,0:57:77:0,77,1652 0/1:43,4:47:21:21,0,1143 0/1:44,5:49:11:11,0,1198 0/0:51,4:55:33:0,33,1319 0/1:29,5:34:25:25,0,716 0/0:32,0:32:93:0,93,1395 0/1:41,7:48:99:117,0,1052 0/1:28,7:35:73:73,0,693 0/1:79,12:91:79:79,0,2051 -chr9 141127790 rs371587150 AG A 1318.73 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=0.455;DB;DP=533;ExcessHet=28.3816;FS=0;InbreedingCoeff=-1;MLEAC=7;MLEAF=0.318;MQ=55.53;MQRankSum=-4.96;NEGATIVE_TRAIN_SITE;QD=2.67;ReadPosRankSum=-1.09;SOR=0.694;VQSLOD=-0.666;culprit=MQ;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000446912|lincRNA||3/8|ENST00000446912.2:n.906+6241del|||||||||1||HGNC|34080|YES||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM157B|ENSG00000233013|Transcript|ENST00000540522|lincRNA||6/6|ENST00000540522.1:n.1175+3518del|||||||||1||HGNC|34080|||||;cadd_phred=-1;gno_non_neuro_af_all=0.138235;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.106121;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:32,5:42:40:98,40,1003 0/1:32,10:44:99:207,0,942 0/0:29,0:33:83:83,170,1724 0/1:40,5:50:5:52,0,1205 0/1:35,9:44:99:173,0,1040 0/0:24,6:38:99:234,104,825 0/1:35,6:41:82:82,0,1051 0/0:57,0:62:37:37,235,4839 0/1:28,10:38:99:227,0,828 0/1:33,12:45:99:267,0,973 0/1:40,16:56:99:366,0,1169 -chr10 38817730 rs149479787 G A 9006.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.153;DB;DP=4238;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=53.89;MQRankSum=0.051;NEGATIVE_TRAIN_SITE;QD=3.46;ReadPosRankSum=-0.069;SOR=0.673;VQSLOD=-2.741;culprit=MQ;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:416,0:416:99:.:.:0,120,1800:. 0/1:187,35:222:99:.:.:585,0,7694:. 0/0:423,0:423:99:.:.:0,120,1800:. 0|1:174,40:214:99:0|1:38817616_G_C:798,0,7102:38817616 0/1:508,53:561:99:.:.:298,0,20661:. 0/0:411,0:411:99:.:.:0,120,1800:. 0|1:142,47:189:99:0|1:38817616_G_C:1248,0,5620:38817616 0|0:239,17:256:38:0|1:38817730_G_A:0,38,9939:38817730 0/1:503,86:589:99:.:.:1222,0,20411:. 0|1:310,94:404:99:0|1:38817730_G_A:2872,0,12405:38817730 0|1:339,85:424:99:0|1:38817730_G_A:2001,0,13773:38817730 -chr10 47085032 rs10532119;rs147157851 CTT C 14192.1 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=842;ExcessHet=3.0103;FS=32.53;InbreedingCoeff=nan;MLEAC=7;MLEAF=0.318;MQ=60.1;MQRankSum=0;QD=23.04;ReadPosRankSum=0.246;SOR=0.644;VQSLOD=3.51;culprit=MQRankSum;CSQ=-|intron_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000374312|protein_coding||1/2|ENST00000374312.1:c.-215-485_-215-484del|||||||||1||HGNC|9329|YES|CCDS31193.1|||,-|upstream_gene_variant|MODIFIER|NPY4R|ENSG00000204174|Transcript|ENST00000395716|protein_coding|||||||||||630|1||HGNC|9329||CCDS31193.1|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|LINC00842|ENSG00000223477|Transcript|ENST00000503031|lincRNA||2/3|ENST00000503031.1:n.254-12055_254-12054del|||||||||-1||HGNC|44989|||||;cadd_phred=-1;gno_non_neuro_af_all=0.175121;gno_non_neuro_af_nfe=0.183934;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_nfe=3;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:6,0:83:99:1361,1455,2078 0/1:1,9:42:99:1584,1107,1009 0/0:5,0:61:99:1132,1216,1656 0/1:3,9:50:99:1232,995,1287 0/1:5,19:78:43:1206,507,496 0/0:0,14:61:99:1305,580,491 0/1:3,17:62:47:1576,745,612 0/0:5,0:42:99:755,832,1188 0/1:0,12:41:99:1462,921,811 0/1:5,9:62:90:1165,916,1177 0/1:0,8:40:99:1421,970,876 -chr10 51484678 . C A 1209.47 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.757;DP=407;ExcessHet=9.0714;FS=125.328;InbreedingCoeff=-0.4676;MLEAC=7;MLEAF=0.318;MQ=46.81;MQRankSum=-1.797;QD=4.38;ReadPosRankSum=-0.015;SOR=7.658;VQSLOD=-140.8;culprit=SOR;CSQ=A|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1301G>T|||||||||-1||HGNC|23465|YES|CCDS41524.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0755986;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0770628;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:35,0:35:99:.:.:0,99,1166:. 0|1:33,6:39:99:0|1:51484678_C_A:153,0,1997:51484678 0/0:27,0:27:42:.:.:0,42,759:. 0|1:42,7:49:99:0|1:51484678_C_A:167,0,2552:51484678 0|1:40,6:46:99:0|1:51484678_C_A:132,0,2324:51484678 0/0:30,0:30:21:.:.:0,21,853:. 0|1:19,3:22:69:0|1:51484678_C_A:69,0,1175:51484678 0/0:37,0:37:27:.:.:0,27,1098:. 0|1:29,10:39:99:0|1:51484678_C_A:333,0,1188:51484678 0|1:27,6:33:99:0|1:51484678_C_A:202,0,1469:51484678 0|1:41,7:48:99:0|1:51484678_C_A:171,0,1647:51484678 -chr10 51484680 . C T 1209.45 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=1.26;DP=406;ExcessHet=9.0714;FS=128.545;InbreedingCoeff=-0.4672;MLEAC=7;MLEAF=0.318;MQ=46.76;MQRankSum=-1.739;QD=4.41;ReadPosRankSum=0.194;SOR=7.701;VQSLOD=-146.4;culprit=SOR;CSQ=T|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1299G>A|||||||||-1||HGNC|23465|YES|CCDS41524.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.0797723;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0813679;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:35,0:35:99:.:.:0,99,1166:. 0|1:33,6:39:99:0|1:51484678_C_A:153,0,1997:51484678 0/0:28,0:28:78:.:.:0,78,1170:. 0|1:42,7:49:99:0|1:51484678_C_A:167,0,2552:51484678 0|1:39,6:45:99:0|1:51484678_C_A:132,0,2324:51484678 0/0:31,0:31:23:.:.:0,23,827:. 0|1:19,3:22:69:0|1:51484678_C_A:69,0,1175:51484678 0/0:36,0:36:39:.:.:0,39,1072:. 0|1:29,10:39:99:0|1:51484678_C_A:333,0,1188:51484678 0|1:26,7:33:99:0|1:51484678_C_A:202,0,1469:51484678 0|1:40,7:47:99:0|1:51484678_C_A:171,0,1647:51484678 -chr10 51484776 rs146274111;rs66470138 TTA T 1358.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=370;ExcessHet=9.0714;FS=52.172;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=35.31;MQRankSum=-0.438;QD=5.86;ReadPosRankSum=-0.742;SOR=3.021;VQSLOD=6.76;culprit=FS;CSQ=-|intron_variant|MODIFIER|AGAP7|ENSG00000204169|Transcript|ENST00000374095|protein_coding||1/6|ENST00000374095.5:c.223+1201_223+1202del|||||||||-1||HGNC|23465|YES|CCDS41524.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.269477;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.274031;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:29,0:29:81:0,81,1215 0/1:30,7:37:99:204,0,1301 0/0:30,0:30:84:0,84,1260 0/1:28,14:42:99:493,0,1170 0/1:48,9:57:99:213,0,2058 0/0:35,0:35:93:0,93,1395 0/1:19,5:24:99:153,0,827 0/0:37,0:37:99:0,102,1530 0/1:18,5:23:99:156,0,741 0/1:18,3:21:61:61,0,781 0/1:24,4:28:96:96,0,985 -chr11 134629969 rs79371799 A C 4268.94 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.254;DB;DP=587;ExcessHet=9.0714;FS=38.555;InbreedingCoeff=-0.5714;MLEAC=8;MLEAF=0.364;MQ=50.54;MQRankSum=0.22;NEGATIVE_TRAIN_SITE;QD=10.67;ReadPosRankSum=-1.48;SOR=1.328;VQSLOD=-12.21;culprit=MQ;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-999A>C|||||||||1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.389133;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.396508;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:73,0:73:0:.:.:0,0,1454:. 0|1:22,12:34:99:0|1:134629969_A_C:370,0,1386:134629969 0/0:60,0:60:0:.:.:0,0,963:. 0|1:36,7:43:99:0|1:134629969_A_C:169,0,1428:134629969 0|1:39,7:46:67:0|1:134629969_A_C:67,0,1650:134629969 0/0:23,0:23:69:.:.:0,69,749:. 0|1:27,9:36:99:0|1:134629969_A_C:244,0,1008:134629969 0/0:30,0:30:81:.:.:0,81,1215:. 0|1:50,11:61:99:0|1:134629969_A_C:163,0,2086:134629969 0|1:42,41:83:99:0|1:134629969_A_C:1531,0,1571:134629969 0|1:47,50:97:99:0|1:134629969_A_C:1734,0,1870:134629969 -chr11 134629972 rs113877482 A C 4299.74 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.511;DB;DP=570;ExcessHet=11.8014;FS=24.473;InbreedingCoeff=-0.6923;MLEAC=8;MLEAF=0.364;MQ=50.58;MQRankSum=0.169;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=-0.579;SOR=1.466;VQSLOD=-5.583;culprit=MQ;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-469N6.1|ENSG00000251226|Transcript|ENST00000513405|lincRNA||1/1|ENST00000513405.1:n.948-996A>C|||||||||1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.411614;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.424807;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:66,0:66:0:.:.:0,0,1201:. 0|1:23,12:35:99:0|1:134629969_A_C:370,0,1386:134629969 0/0:55,0:55:0:.:.:0,0,313:. 0|1:36,7:43:99:0|1:134629969_A_C:169,0,1428:134629969 0|1:37,6:43:59:0|1:134629969_A_C:59,0,1688:134629969 0/0:22,0:22:66:.:.:0,66,755:. 0|1:27,9:36:99:0|1:134629969_A_C:244,0,1008:134629969 0|0:29,0:35:99:0|1:134629955_C_T:165,252,1474:134629955 0|1:51,8:59:99:0|1:134629969_A_C:123,0,2215:134629969 0|1:40,39:79:99:0|1:134629969_A_C:1503,0,1543:134629969 0|1:50,46:96:99:0|1:134629969_A_C:1684,0,2044:134629969 -chr12 334342 rs11835796 C T 4739.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.139;DB;DP=491;ExcessHet=9.0714;FS=1.344;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.099;SOR=0.597;VQSLOD=23.72;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000343164|protein_coding||9/14|ENST00000343164.4:c.1061-663G>A|||||||||-1||HGNC|11046|YES|CCDS8502.1|||,T|intron_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000445055|protein_coding||7/12|ENST00000445055.2:c.785-663G>A|||||||||-1||HGNC|11046||CCDS53729.1|||,T|upstream_gene_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000539668|processed_transcript|||||||||||745|-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542379|processed_transcript||2/2|ENST00000542379.1:n.220-1942G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000542947|retained_intron||2/2|ENST00000542947.1:n.445-663G>A|||||||||-1||HGNC|11046|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A13|ENSG00000010379|Transcript|ENST00000543722|retained_intron||1/2|ENST00000543722.1:n.291-663G>A|||||||||-1||HGNC|11046|||||;cadd_phred=-1;gno_non_neuro_af_all=0.301969;gno_non_neuro_af_nfe=0.283645;gno_non_neuro_nhomalt_all=986;gno_non_neuro_nhomalt_nfe=555;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,120,1800 0/1:11,26:37:99:763,0,246 0/0:41,0:41:99:0,106,1381 0/1:27,25:52:99:693,0,772 0/1:17,26:43:99:720,0,462 0/0:39,0:39:99:0,99,1286 0/1:24,17:41:99:458,0,709 0/0:43,0:43:99:0,99,1390 0/1:27,25:52:99:672,0,782 0/1:25,16:41:99:433,0,715 0/1:24,35:59:99:1018,0,657 -chr12 2033347 rs10848595 C T 3645.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=2.3;DB;DP=447;ExcessHet=9.0714;FS=3.976;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=51.96;MQRankSum=-2.758;NEGATIVE_TRAIN_SITE;QD=13.16;ReadPosRankSum=0.482;SOR=0.918;VQSLOD=-2.23;culprit=MQ;CSQ=T|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||1314|1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.481677;gno_non_neuro_af_nfe=0.556349;gno_non_neuro_nhomalt_all=2670;gno_non_neuro_nhomalt_nfe=2075;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,115,1395 0/1:24,11:35:99:277,0,637 0/0:42,0:42:91:0,91,1310 0/1:24,23:47:99:638,0,606 0/1:19,22:41:99:591,0,527 0/0:45,0:45:99:0,116,1514 0/1:10,14:24:99:405,0,265 0/0:38,0:38:99:0,100,1232 0/1:26,14:40:99:356,0,673 0/1:19,19:38:99:536,0,426 0/1:22,30:52:99:860,0,505 -chr12 2036141 rs11610387 T C 3889.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-2.006;DB;DP=477;ExcessHet=9.0714;FS=24.678;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.12;ReadPosRankSum=0.49;SOR=0.465;VQSLOD=16.93;culprit=MQRankSum;CSQ=C|downstream_gene_variant|MODIFIER|LINC00940|ENSG00000235049|Transcript|ENST00000418006|lincRNA|||||||||||2227|-1||HGNC|48634|YES||||,C|downstream_gene_variant|MODIFIER|RP5-1096D14.3|ENSG00000256706|Transcript|ENST00000544163|antisense|||||||||||4108|1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.469936;gno_non_neuro_af_nfe=0.558798;gno_non_neuro_nhomalt_all=2687;gno_non_neuro_nhomalt_nfe=2135;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:40,0:40:99:0,111,1405 0/1:17,18:35:99:480,0,486 0/0:38,0:38:99:0,100,1291 0/1:26,30:56:99:840,0,736 0/1:27,13:40:99:332,0,808 0/0:36,0:36:99:0,99,1232 0/1:21,15:36:99:413,0,622 0/0:41,0:41:99:0,108,1391 0/1:24,26:50:99:633,0,684 0/1:22,18:40:99:415,0,644 0/1:31,33:64:99:794,0,854 -chr12 5569271 rs7314794 C T 4518.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=466;ExcessHet=9.0714;FS=16.139;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=-0.783;SOR=0.967;VQSLOD=21.94;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000423158|protein_coding||1/1|ENST00000423158.3:c.18+27763C>T|||||||||1||HGNC|8023|YES|CCDS44806.1|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000535299|processed_transcript||1/4|ENST00000535299.1:n.231+27763C>T|||||||||1||HGNC|8023|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NTF3|ENSG00000185652|Transcript|ENST00000543548|processed_transcript||1/1|ENST00000543548.1:n.208+26773C>T|||||||||1||HGNC|8023|||||;cadd_phred=-1;gno_non_neuro_af_all=0.617836;gno_non_neuro_af_nfe=0.555637;gno_non_neuro_nhomalt_all=4097;gno_non_neuro_nhomalt_nfe=2064;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,105,1405 0/1:15,19:34:99:491,0,400 0/0:37,0:37:99:0,101,1229 0/1:25,23:48:99:610,0,680 0/1:15,25:40:99:749,0,390 0/0:40,0:40:99:0,99,1336 0/1:15,8:23:99:198,0,429 0/0:31,0:31:90:0,90,1350 0/1:24,24:48:99:688,0,685 0/1:27,27:54:99:774,0,765 0/1:31,37:68:99:1026,0,839 -chr12 6744864 rs4764623 G C 3605.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.314;DB;DP=446;ExcessHet=9.0714;FS=10.015;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=-0.191;SOR=0.373;VQSLOD=23.73;culprit=MQRankSum;CSQ=C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000229243|protein_coding|||||||||||2377|-1||HGNC|17195|YES|CCDS8554.1|||,C|intron_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000329858|protein_coding||1/1|ENST00000329858.4:c.-217+209C>G|||||||||-1||HGNC|13307|YES|CCDS8553.1|||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000414226|protein_coding|||||||||||2462|-1||HGNC|17195|||||,C|upstream_gene_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000431922|protein_coding|||||||||||4049|-1||HGNC|13307||CCDS8553.1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|LPAR5|ENSG00000184574|Transcript|ENST00000540335|processed_transcript||1/2|ENST00000540335.1:n.54+209C>G|||||||||-1||HGNC|13307|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000540513|processed_transcript|||||||||||2377|-1||HGNC|17195|||||,C|downstream_gene_variant|MODIFIER|ACRBP|ENSG00000111644|Transcript|ENST00000542357|processed_transcript|||||||||||2812|-1||HGNC|17195|||||;cadd_phred=-1;gno_non_neuro_af_all=0.536383;gno_non_neuro_af_nfe=0.568792;gno_non_neuro_nhomalt_all=3155;gno_non_neuro_nhomalt_nfe=2202;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1305 0/1:17,7:24:99:172,0,494 0/0:37,0:37:99:0,102,1530 0/1:19,27:46:99:781,0,467 0/1:27,20:47:99:553,0,797 0/0:31,0:31:90:0,90,1350 0/1:15,22:37:99:559,0,409 0/0:37,0:37:99:0,100,1230 0/1:29,21:50:99:560,0,835 0/1:21,11:32:99:276,0,631 0/1:39,28:67:99:722,0,1068 -chr12 8335722 rs11043797 A T 3602.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.355;DB;DP=476;ExcessHet=9.0714;FS=3.734;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.49;MQRankSum=0;QD=16.37;ReadPosRankSum=0.309;SOR=0.966;VQSLOD=3.93;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000359286|protein_coding|||||||||||3080|1||HGNC|32281|YES|CCDS31737.1|||,T|intron_variant|MODIFIER|ZNF705A|ENSG00000196946|Transcript|ENST00000398526|protein_coding||2/2|ENST00000398526.2:c.274-5346A>T|||||||||1|cds_start_NF|HGNC|32281|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000454799|antisense||1/6|ENST00000454799.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000456135|antisense||1/3|ENST00000456135.2:n.544+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000541558|antisense||1/7|ENST00000541558.1:n.484+2374A>T|||||||||1||HGNC|21644|||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM66C|ENSG00000226711|Transcript|ENST00000544214|antisense||1/5|ENST00000544214.1:n.531+2374A>T|||||||||1||HGNC|21644|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.138584;gno_non_neuro_af_nfe=0.128167;gno_non_neuro_nhomalt_all=193;gno_non_neuro_nhomalt_nfe=100;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:48,0:48:99:0,99,1485 0/1:19,8:27:99:231,0,672 0/0:30,0:30:63:0,63,945 0/1:10,13:23:99:506,0,701 0/1:21,12:33:99:483,0,707 0/0:49,0:49:90:0,90,1350 0/1:12,14:26:99:388,0,677 0/0:17,0:17:51:0,51,744 0/1:24,13:37:99:537,0,936 0/1:13,11:24:99:551,0,1013 0/1:29,21:50:99:924,0,1000 -chr12 9739997 rs7955007 C A 4151.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.066;DB;DP=433;ExcessHet=9.0714;FS=0.418;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.93;ReadPosRankSum=0.399;SOR=0.665;VQSLOD=23.76;culprit=MQRankSum;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.466522;gno_non_neuro_af_nfe=0.493146;gno_non_neuro_nhomalt_all=2305;gno_non_neuro_nhomalt_nfe=1620;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1197 0/1:20,16:36:99:448,0,576 0/0:35,0:35:99:0,99,1485 0/1:23,24:47:99:669,0,638 0/1:17,15:32:99:426,0,385 0/0:27,0:27:81:0,81,919 0/1:14,18:32:99:505,0,380 0/0:38,0:38:99:0,108,1451 0/1:25,24:49:99:640,0,718 0/1:19,17:36:99:473,0,551 0/1:29,37:66:99:1008,0,798 -chr12 9740839 rs7137213 G A 4647.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.978;DB;DP=463;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.14;ReadPosRankSum=-0.321;SOR=0.68;VQSLOD=23.84;culprit=MQRankSum;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.395541;gno_non_neuro_af_nfe=0.452966;gno_non_neuro_nhomalt_all=1773;gno_non_neuro_nhomalt_nfe=1356;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,101,1445 0/1:19,15:34:99:419,0,518 0/0:39,0:39:99:0,111,1665 0/1:18,26:44:99:751,0,493 0/1:22,19:41:99:537,0,631 0/0:41,0:41:99:0,105,1366 0/1:13,24:37:99:723,0,321 0/0:33,0:33:99:0,99,1147 0/1:18,19:37:99:547,0,513 0/1:25,16:41:99:415,0,731 0/1:30,43:73:99:1273,0,801 -chr12 9745571 rs4763635 A G 4058.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.912;DB;DP=489;ExcessHet=9.0714;FS=10.836;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=11.87;ReadPosRankSum=-0.08;SOR=1.147;VQSLOD=23.83;culprit=MQRankSum;CSQ=G|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||1576|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.446882;gno_non_neuro_af_nfe=0.493154;gno_non_neuro_nhomalt_all=2176;gno_non_neuro_nhomalt_nfe=1624;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,100,1277 0/1:9,20:29:99:558,0,227 0/0:37,0:37:99:0,99,1485 0/1:17,26:43:99:750,0,462 0/1:24,21:45:99:575,0,689 0/0:37,0:37:99:0,100,1212 0/1:14,15:29:99:409,0,390 0/0:34,0:34:78:0,78,1113 0/1:38,28:66:99:564,0,1123 0/1:31,25:56:99:516,0,874 0/1:41,33:74:99:704,0,1202 -chr12 9746600 rs10771918 T C 5327.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.035;DB;DP=495;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.96;ReadPosRankSum=0.73;SOR=0.682;VQSLOD=23.48;culprit=MQRankSum;CSQ=C|downstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||547|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.446344;gno_non_neuro_af_nfe=0.493239;gno_non_neuro_nhomalt_all=2177;gno_non_neuro_nhomalt_nfe=1629;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,105,1575 0/1:20,20:40:99:555,0,555 0/0:26,0:26:72:0,72,894 0/1:24,27:51:99:785,0,660 0/1:16,20:36:99:567,0,428 0/0:35,0:35:99:0,99,1272 0/1:15,15:30:99:411,0,411 0/0:39,0:39:99:0,99,1356 0/1:31,36:67:99:1050,0,876 0/1:30,33:63:99:933,0,854 0/1:33,36:69:99:1044,0,914 -chr12 9747513 rs2058428 G A 17315.7 PASS AC=7;AF=0.318;AN=22;DB;DP=454;ExcessHet=3.0103;FS=0;InbreedingCoeff=nan;MLEAC=7;MLEAF=0.318;MQ=60.05;QD=30.83;SOR=0.831;VQSLOD=3.44;culprit=QD;CSQ=A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*357C>T||1082/1448|||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.586462;gno_non_neuro_af_nfe=0.570162;gno_non_neuro_nhomalt_all=3709;gno_non_neuro_nhomalt_nfe=2184;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0|0:0,0:43:99:1|1:9747513_GTGC_G:1935,1935,1935:9747513 0/1:0,8:18:99:.:.:671,417,393:. 0|0:0,0:43:99:1|1:9747513_GTGC_G:1935,1935,1935:9747513 0/1:0,17:37:99:.:.:1356,829,786:. 0/1:0,25:43:99:.:.:1577,806,740:. 0|0:0,0:42:99:1|1:9747513_GTGC_G:1891,1891,1891:9747513 0/1:0,12:29:99:.:.:1049,688,652:. 0|0:0,0:36:99:1|1:9747513_GTGC_G:1598,1598,1598:9747513 0/1:0,33:54:99:.:.:1826,858,760:. 0/1:0,28:47:99:.:.:1542,785,711:. 0/1:0,28:55:99:.:.:1899,1096,1051:. -chr12 9747557 rs2058427 T A 3876.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.22;DB;DP=435;ExcessHet=9.0714;FS=6.421;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.99;ReadPosRankSum=0.122;SOR=1.035;VQSLOD=24.26;culprit=MQRankSum;CSQ=A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*313A>T||1038/1448|||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.471313;gno_non_neuro_af_nfe=0.492262;gno_non_neuro_nhomalt_all=2348;gno_non_neuro_nhomalt_nfe=1613;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1485 0/1:12,8:20:99:207,0,357 0/0:47,0:47:99:0,109,1528 0/1:21,16:37:99:444,0,594 0/1:24,19:43:99:511,0,675 0/0:37,0:37:96:0,96,1440 0/1:14,12:26:99:339,0,387 0/0:36,0:36:99:0,99,1485 0/1:19,31:50:99:880,0,510 0/1:22,19:41:99:537,0,631 0/1:25,35:60:99:976,0,677 -chr12 9747676 rs2058426 G A 4642.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.615;DB;DP=483;ExcessHet=9.0714;FS=8.229;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.15;ReadPosRankSum=0.796;SOR=0.422;VQSLOD=23.96;culprit=MQRankSum;CSQ=A|3_prime_UTR_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|6/6||ENST00000229402.3:c.*194C>T||919/1448|||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.474057;gno_non_neuro_af_nfe=0.495801;gno_non_neuro_nhomalt_all=2374;gno_non_neuro_nhomalt_nfe=1634;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,105,1271 0/1:23,10:33:99:249,0,611 0/0:47,0:47:99:0,109,1528 0/1:24,13:37:99:331,0,673 0/1:20,25:45:99:693,0,550 0/0:37,0:37:99:0,99,1391 0/1:15,18:33:99:527,0,353 0/0:35,0:35:99:0,102,1167 0/1:16,41:57:99:1234,0,384 0/1:28,25:53:99:665,0,793 0/1:36,34:70:99:961,0,1040 -chr12 9748572 rs2241005 T C 5259.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.149;DB;DP=488;ExcessHet=9.0714;FS=19.998;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=-0.324;SOR=0.71;VQSLOD=20.5;culprit=MQRankSum;CSQ=C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.531-555A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.490104;gno_non_neuro_af_nfe=0.497058;gno_non_neuro_nhomalt_all=2536;gno_non_neuro_nhomalt_nfe=1645;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:78:0,78,1103 0/1:11,30:41:99:885,0,225 0/0:35,0:35:99:0,102,1226 0/1:20,11:31:99:259,0,592 0/1:31,21:52:99:574,0,919 0/0:35,0:35:99:0,99,1232 0/1:20,24:44:99:680,0,541 0/0:35,0:35:99:0,99,1485 0/1:24,32:56:99:942,0,656 0/1:21,26:47:99:728,0,587 0/1:35,42:77:99:1209,0,974 -chr12 9749543 rs985913 G A 4909.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.812;DB;DP=526;ExcessHet=9.0714;FS=3.932;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.3;ReadPosRankSum=-0.296;SOR=0.879;VQSLOD=23.49;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+1099C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.321233;gno_non_neuro_af_nfe=0.362097;gno_non_neuro_nhomalt_all=1192;gno_non_neuro_nhomalt_nfe=872;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:37,0:37:99:.:.:0,99,1351:. 0|1:21,18:39:99:1|0:9749535_C_T:488,0,807:9749535 0/0:40,0:40:99:.:.:0,105,1322:. 0/1:21,33:54:99:.:.:944,0,782:. 0|1:20,14:34:99:1|0:9749535_C_T:384,0,787:9749535 0/0:37,0:37:99:.:.:0,99,1485:. 0|1:20,22:42:99:1|0:9749535_C_T:638,0,763:9749535 0/0:41,0:41:99:.:.:0,108,1426:. 0|1:37,26:63:99:1|0:9749535_C_T:711,0,1466:9749535 0/1:29,30:59:99:.:.:841,0,1149:. 0|1:43,35:78:99:1|0:9749535_C_T:921,0,1680:9749535 -chr12 9749682 rs985912 T C 5313.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.239;DB;DP=496;ExcessHet=9.0714;FS=2.311;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-0.203;SOR=0.828;VQSLOD=23.45;culprit=MQRankSum;CSQ=C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+960A>G|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.4901;gno_non_neuro_af_nfe=0.496908;gno_non_neuro_nhomalt_all=2537;gno_non_neuro_nhomalt_nfe=1643;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,102,1226 0/1:16,20:36:99:541,0,428 0/0:40,0:40:99:0,105,1322 0/1:18,27:45:99:740,0,490 0/1:13,20:33:99:596,0,351 0/0:35,0:35:99:0,99,1231 0/1:10,20:30:99:556,0,238 0/0:41,0:41:99:0,108,1426 0/1:34,34:68:99:977,0,972 0/1:26,29:55:99:833,0,732 0/1:37,39:76:99:1088,0,1058 -chr12 9749726 rs985911 G T 4917.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.299;DB;DP=498;ExcessHet=9.0714;FS=0.385;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.021;SOR=0.67;VQSLOD=23.47;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||5/5|ENST00000229402.3:c.530+916C>A|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.490522;gno_non_neuro_af_nfe=0.497572;gno_non_neuro_nhomalt_all=2538;gno_non_neuro_nhomalt_nfe=1647;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,102,1226 0/1:15,14:29:99:400,0,399 0/0:37,0:37:99:0,102,1415 0/1:22,25:47:99:667,0,593 0/1:15,19:34:99:557,0,384 0/0:35,0:35:99:0,99,1231 0/1:12,21:33:99:630,0,298 0/0:40,0:40:99:0,99,1316 0/1:38,28:66:99:765,0,1110 0/1:27,32:59:99:905,0,760 0/1:43,37:80:99:1011,0,1208 -chr12 9752576 rs55659351;rs67712680 TAA T 15028.7 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=1.64;DB;DP=435;ExcessHet=3.0103;FS=0;InbreedingCoeff=nan;MLEAC=7;MLEAF=0.318;MQ=60.07;MQRankSum=0.371;NEGATIVE_TRAIN_SITE;QD=33.56;ReadPosRankSum=1.73;SOR=1.108;VQSLOD=-0.6292;culprit=MQRankSum;CSQ=-|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||2/5|ENST00000229402.3:c.185-141_185-140del|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.468831;gno_non_neuro_af_nfe=0.507347;gno_non_neuro_nhomalt_all=1899;gno_non_neuro_nhomalt_nfe=1416;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:0,0:42:99:1868,1868,1868 0/1:0,10:24:99:845,351,293 0/0:0,0:33:99:1444,1444,1444 0/1:0,10:24:99:910,363,291 0/1:0,20:38:99:1405,470,357 0/0:0,0:31:93:1395,1395,1395 0/1:1,17:27:99:910,215,155 0/0:1,0:30:80:1255,1257,1264 0/1:0,23:50:99:1848,704,556 0/1:0,20:40:99:1493,523,404 0/1:0,18:44:99:1619,649,537 -chr12 9755905 rs4763657 G A 4896.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.411;DB;DP=474;ExcessHet=9.0714;FS=11.705;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.03;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-0.815;SOR=1.213;VQSLOD=7.16;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1710C>T|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.371155;gno_non_neuro_af_nfe=0.369347;gno_non_neuro_nhomalt_all=1482;gno_non_neuro_nhomalt_nfe=897;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,104,1381:. 0|1:13,28:41:99:1|0:9755904_C_T:790,0,427:9755904 0/0:32,0:32:90:.:.:0,90,1350:. 0|1:20,29:49:99:1|0:9755904_C_T:803,0,774:9755904 0|1:16,29:45:99:1|0:9755904_C_T:823,0,585:9755904 0/0:40,0:40:99:.:.:0,99,1352:. 0|1:15,17:32:99:1|0:9755904_C_T:475,0,579:9755904 0/0:42,0:42:99:.:.:0,111,1665:. 0/1:24,24:48:99:.:.:679,0,590:. 0|1:23,23:46:99:1|0:9755904_C_T:641,0,886:9755904 0|1:30,25:55:99:1|0:9755904_C_T:703,0,1184:9755904 -chr12 9756021 rs148830030;rs56793467 C CTATT 4896.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=463;ExcessHet=9.0714;FS=2.879;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.03;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=20.84;ReadPosRankSum=-0.093;SOR=0.847;VQSLOD=10.46;culprit=MQRankSum;CSQ=TATT|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.86-1830_86-1827dup|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.358611;gno_non_neuro_af_nfe=0.357388;gno_non_neuro_nhomalt_all=1344;gno_non_neuro_nhomalt_nfe=823;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,99,1272 0/1:11,17:28:99:716,0,495 0/0:30,0:30:41:0,41,914 0/1:17,18:35:99:681,0,831 0/1:13,16:29:99:662,0,627 0/0:40,0:40:99:0,99,1352 0/1:12,14:26:99:534,0,600 0/0:37,0:37:99:0,102,1301 0/1:24,17:41:99:618,0,1173 0/1:15,20:35:99:740,0,719 0/1:17,24:41:99:963,0,745 -chr12 9759244 rs10667765 T TTA 2615.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.412;DB;DP=333;ExcessHet=9.0714;FS=16.613;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.48;MQRankSum=0;QD=14.14;ReadPosRankSum=-0.403;SOR=0.218;VQSLOD=4.79;culprit=MQRankSum;CSQ=TA|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+1105_85+1106dup|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.460276;gno_non_neuro_af_nfe=0.480533;gno_non_neuro_nhomalt_all=1430;gno_non_neuro_nhomalt_nfe=1075;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:30,0:30:81:.:.:0,81,1215:. 0/1:10,8:18:99:.:.:235,0,358:. 0/0:28,0:28:84:.:.:0,84,933:. 0/1:13,10:23:99:.:.:291,0,499:. 0/1:19,13:32:99:.:.:373,0,688:. 0/0:25,0:25:50:.:.:0,50,789:. 0|1:13,13:26:99:0|1:9759244_T_TTA:397,0,480:9759244 0/0:26,0:26:72:.:.:0,72,1080:. 0/1:10,15:25:99:.:.:462,0,309:. 0/1:7,12:19:99:.:.:395,0,225:. 0|1:25,17:42:99:0|1:9759244_T_TTA:480,0,872:9759244 -chr12 9759465 rs4763675 A C 3293.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.207;DB;DP=411;ExcessHet=9.0714;FS=3.51;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.52;ReadPosRankSum=-0.122;SOR=0.517;VQSLOD=23.24;culprit=MQRankSum;CSQ=C|intron_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding||1/5|ENST00000229402.3:c.85+886T>G|||||||||-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.378239;gno_non_neuro_af_nfe=0.421036;gno_non_neuro_nhomalt_all=1567;gno_non_neuro_nhomalt_nfe=1108;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:40,0:40:91:0,91,1252 0/1:9,13:22:99:386,0,247 0/0:30,0:30:81:0,81,1215 0/1:19,19:38:99:526,0,516 0/1:29,14:43:99:357,0,858 0/0:32,0:32:46:0,46,943 0/1:12,15:27:99:395,0,326 0/0:44,0:44:73:0,73,1340 0/1:19,17:36:99:461,0,542 0/1:22,16:38:99:432,0,607 0/1:31,28:59:99:754,0,845 -chr12 9761465 rs4763678 C G 3228.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.651;DB;DP=393;ExcessHet=9.0714;FS=0.939;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=52.36;MQRankSum=-1.34;NEGATIVE_TRAIN_SITE;QD=12.23;ReadPosRankSum=0.243;SOR=0.732;VQSLOD=-2.365;culprit=MQ;CSQ=G|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||983|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.380015;gno_non_neuro_af_nfe=0.423276;gno_non_neuro_nhomalt_all=1658;gno_non_neuro_nhomalt_nfe=1180;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:30,0:30:87:0,87,1305 0/1:22,14:36:99:359,0,622 0/0:32,0:32:90:0,90,1042 0/1:17,5:22:99:108,0,515 0/1:22,20:42:99:568,0,604 0/0:34,0:34:99:0,102,1132 0/1:17,15:32:99:424,0,495 0/0:29,0:29:84:0,84,988 0/1:30,24:54:99:672,0,864 0/1:23,16:39:99:439,0,652 0/1:16,23:39:99:676,0,434 -chr12 9763589 rs7302021 C T 4720.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.07;DB;DP=489;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.98;MQRankSum=0;QD=14.01;ReadPosRankSum=-0.276;SOR=0.678;VQSLOD=7.72;culprit=MQRankSum;CSQ=T|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3107|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.37913;gno_non_neuro_af_nfe=0.422091;gno_non_neuro_nhomalt_all=1660;gno_non_neuro_nhomalt_nfe=1181;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,120,1800:. 0/1:15,17:32:99:.:.:495,0,405:. 0/0:35,0:35:99:.:.:0,99,1201:. 0/1:17,28:45:99:.:.:768,0,456:. 0/1:21,20:41:99:.:.:532,0,607:. 0/0:38,0:38:99:.:.:0,100,1242:. 0/1:22,18:40:99:.:.:506,0,604:. 0/0:37,0:37:99:.:.:0,108,1301:. 0|1:27,29:56:99:0|1:9763589_C_T:836,0,1048:9763589 0/1:28,24:52:99:.:.:658,0,817:. 0/1:37,34:71:99:.:.:943,0,1033:. -chr12 9763737 rs7301291 G A 5076.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.508;DB;DP=448;ExcessHet=9.0714;FS=7;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.78;MQRankSum=0;QD=16.81;ReadPosRankSum=0.294;SOR=0.79;VQSLOD=6.83;culprit=MQRankSum;CSQ=A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||3255|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.378565;gno_non_neuro_af_nfe=0.421863;gno_non_neuro_nhomalt_all=1653;gno_non_neuro_nhomalt_nfe=1176;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,102,1320 0/1:11,22:33:99:641,0,274 0/0:34,0:34:99:0,99,1142 0/1:18,22:40:99:614,0,471 0/1:24,28:52:99:796,0,658 0/0:36,0:36:99:0,100,1240 0/1:7,26:33:99:755,0,144 0/0:39,0:39:99:0,105,1320 0/1:22,19:41:99:537,0,541 0/1:15,26:41:99:751,0,308 0/1:27,35:62:99:1000,0,562 -chr12 9764897 rs139642020 G A 4206.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.64;DB;DP=450;ExcessHet=9.0714;FS=0.867;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=58.53;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.7;ReadPosRankSum=-0.967;SOR=0.626;VQSLOD=4.92;culprit=MQRankSum;CSQ=A|upstream_gene_variant|MODIFIER|KLRB1|ENSG00000111796|Transcript|ENST00000229402|protein_coding|||||||||||4415|-1||HGNC|6373|YES|CCDS8601.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.379082;gno_non_neuro_af_nfe=0.422317;gno_non_neuro_nhomalt_all=1658;gno_non_neuro_nhomalt_nfe=1178;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,102,1216 0/1:13,13:26:99:354,0,364 0/0:37,0:37:99:0,99,1401 0/1:24,20:44:99:532,0,632 0/1:19,22:41:99:621,0,536 0/0:38,0:38:80:0,80,1211 0/1:20,16:36:99:403,0,577 0/0:26,0:26:53:0,53,824 0/1:25,23:48:99:635,0,714 0/1:21,22:43:99:526,0,537 0/1:29,40:69:99:1153,0,770 -chr12 9769429 rs10546600;rs142555042 CAGAG C 2238.36 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.878;DB;DP=341;ExcessHet=9.0714;FS=0.621;InbreedingCoeff=-0.5455;MLEAC=8;MLEAF=0.364;MQ=59.59;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.12;ReadPosRankSum=-0.082;SOR=0.781;VQSLOD=6.29;culprit=MQRankSum;CSQ=-|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.379867;gno_non_neuro_af_nfe=0.42454;gno_non_neuro_nhomalt_all=1287;gno_non_neuro_nhomalt_nfe=922;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:49,0:49:92:0,92,1321 0/1:9,10:19:99:383,0,345 0/0:41,0:41:5:0,5,977 0/1:9,6:15:99:225,0,349 0/1:11,7:18:99:251,0,441 0/0:40,0:40:0:0,0,722 0/1:15,12:27:99:449,0,581 0/0:40,0:40:16:0,16,849 0/1:15,9:24:99:333,0,571 0/1:11,6:17:99:209,0,444 0/1:17,11:28:99:400,0,678 -chr12 9779878 rs115368398 T A 6771.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.15;DB;DP=448;ExcessHet=9.0714;FS=5.097;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.98;MQRankSum=0;QD=21.29;ReadPosRankSum=0.493;SOR=0.473;VQSLOD=7.39;culprit=MQRankSum;CSQ=A|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3054|-1||HGNC|47663|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.377381;gno_non_neuro_af_nfe=0.419781;gno_non_neuro_nhomalt_all=1544;gno_non_neuro_nhomalt_nfe=1098;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:35,0:35:99:.:.:0,102,1530:. 0|1:8,10:18:99:0|1:9779867_CTT_C:428,0,649:9779867 0/0:30,0:30:81:.:.:0,81,1215:. 0|1:18,25:43:99:0|1:9779867_CTT_C:996,0,1559:9779867 0|1:19,23:42:99:0|1:9779867_CTT_C:903,0,1836:9779867 0/0:35,0:35:93:.:.:0,93,1395:. 0|1:19,15:34:99:0|1:9779867_CTT_C:579,0,1774:9779867 0/0:28,0:28:69:.:.:0,69,1035:. 0|1:25,24:49:99:0|1:9779867_CTT_C:678,0,706:9779867 0|1:22,35:57:99:0|1:9779867_CTT_C:1457,0,1942:9779867 0|1:31,44:75:99:0|1:9779867_CTT_C:1748,0,2679:9779867 -chr12 9780206 rs4486710 C T 4786.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=463;ExcessHet=9.0714;FS=1.317;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=56.16;MQRankSum=0;QD=14.86;ReadPosRankSum=-0.038;SOR=0.615;VQSLOD=-0.0261;culprit=MQ;CSQ=T|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3382|-1||HGNC|47663|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.379998;gno_non_neuro_af_nfe=0.422834;gno_non_neuro_nhomalt_all=1668;gno_non_neuro_nhomalt_nfe=1190;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,102,1261 0/1:15,18:33:99:506,0,422 0/0:33,0:33:90:0,90,1350 0/1:23,21:44:99:577,0,637 0/1:30,29:59:99:831,0,855 0/0:37,0:37:99:0,105,1575 0/1:11,16:27:99:475,0,301 0/0:32,0:32:90:0,90,1350 0/1:25,35:60:99:996,0,689 0/1:21,26:47:99:742,0,578 0/1:28,24:52:99:677,0,796 -chr12 9780577 rs72656628 A G 3358.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.863;DB;DP=433;ExcessHet=9.0714;FS=10.22;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=53.72;MQRankSum=-1.397;NEGATIVE_TRAIN_SITE;QD=11.78;ReadPosRankSum=-0.118;SOR=0.395;VQSLOD=-1.207;culprit=MQ;CSQ=G|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||3753|-1||HGNC|47663|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.379642;gno_non_neuro_af_nfe=0.422698;gno_non_neuro_nhomalt_all=1670;gno_non_neuro_nhomalt_nfe=1189;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,102,1261 0/1:21,19:40:99:521,0,565 0/0:40,0:40:99:0,104,1320 0/1:16,19:35:99:525,0,451 0/1:19,23:42:99:633,0,534 0/0:36,0:36:99:0,99,1130 0/1:19,11:30:99:283,0,525 0/0:35,0:35:93:0,93,1395 0/1:24,20:44:99:483,0,702 0/1:22,21:43:99:490,0,616 0/1:31,20:51:99:441,0,923 -chr12 9780843 rs79677075 T C 3731.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.793;DB;DP=448;ExcessHet=9.0714;FS=13.633;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=49.22;MQRankSum=-0.287;NEGATIVE_TRAIN_SITE;QD=12.96;ReadPosRankSum=0.147;SOR=0.321;VQSLOD=-2.572;culprit=MQ;CSQ=C|upstream_gene_variant|MODIFIER|RNU6-700P|ENSG00000212345|Transcript|ENST00000391043|snRNA|||||||||||4019|-1||HGNC|47663|YES||||;cadd_phred=11;gno_non_neuro_af_all=0.378809;gno_non_neuro_af_nfe=0.421603;gno_non_neuro_nhomalt_all=1655;gno_non_neuro_nhomalt_nfe=1174;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,99,1346 0/1:20,13:33:99:352,0,593 0/0:36,0:36:99:0,102,1246 0/1:25,16:41:99:407,0,734 0/1:11,21:32:99:608,0,286 0/0:49,0:49:99:0,114,1585 0/1:17,19:36:99:519,0,483 0/0:36,0:36:99:0,99,1485 0/1:27,21:48:99:566,0,770 0/1:20,18:38:99:481,0,561 0/1:29,31:60:99:816,0,811 -chr12 9997789 rs2012290 A T 4677.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=472;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.39;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.367;SOR=0.71;VQSLOD=6.27;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279544|protein_coding|||||||||||183|1||HGNC|13342|YES|CCDS41750.1|||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000279545|nonsense_mediated_decay|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000324214|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000354855|protein_coding|||||||||||183|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000535631|nonsense_mediated_decay|||||||||||198|1|cds_start_NF|HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000537723|protein_coding|||||||||||533|1||HGNC|13342|||||,T|downstream_gene_variant|MODIFIER|KLRF1|ENSG00000150045|Transcript|ENST00000545196|nonsense_mediated_decay|||||||||||533|1||HGNC|13342|||||;cadd_phred=-1;gno_non_neuro_af_all=0.243354;gno_non_neuro_af_nfe=0.298999;gno_non_neuro_nhomalt_all=721;gno_non_neuro_nhomalt_nfe=601;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:40,0:40:96:0,96,1301 0/1:18,18:36:99:507,0,517 0/0:39,0:39:99:0,103,1277 0/1:19,24:43:99:705,0,521 0/1:22,15:37:99:410,0,613 0/0:31,0:31:90:0,90,1072 0/1:14,20:34:99:593,0,384 0/0:31,0:31:90:0,90,1350 0/1:35,32:67:99:910,0,1015 0/1:28,27:55:99:774,0,783 0/1:31,28:59:99:796,0,900 -chr12 10003185 rs113230156 C T 4666.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.05;DB;DP=470;ExcessHet=9.0714;FS=9.244;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.03;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=-0.293;SOR=1.101;VQSLOD=7.49;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000228438|protein_coding|||||||||||2398|-1||HGNC|2053|YES|CCDS8605.1|||,T|downstream_gene_variant|MODIFIER|CLEC2B|ENSG00000110852|Transcript|ENST00000538152|protein_coding|||||||||||2547|-1||HGNC|2053|||||;cadd_phred=-1;gno_non_neuro_af_all=0.0481495;gno_non_neuro_af_nfe=0.0645566;gno_non_neuro_nhomalt_all=30;gno_non_neuro_nhomalt_nfe=26;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,101,1250 0/1:16,21:37:99:619,0,409 0/0:42,0:42:99:0,100,1302 0/1:20,20:40:99:575,0,550 0/1:17,14:31:99:393,0,498 0/0:41,0:41:99:0,118,1440 0/1:24,27:51:99:736,0,571 0/0:21,0:21:60:0,60,710 0/1:25,25:50:99:689,0,684 0/1:16,17:33:99:482,0,446 0/1:41,42:83:99:1190,0,1093 -chr12 10177037 rs1979593 G A 5246.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=503;ExcessHet=9.0714;FS=1.729;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.78;ReadPosRankSum=-0.345;SOR=0.772;VQSLOD=23.72;culprit=MQRankSum;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-133L14.5|ENSG00000256803|Transcript|ENST00000544225|antisense||2/2|ENST00000544225.1:n.248+3477C>T|||||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.304713;gno_non_neuro_af_nfe=0.348498;gno_non_neuro_nhomalt_all=1069;gno_non_neuro_nhomalt_nfe=821;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1485 0/1:21,22:43:99:595,0,600 0/0:50,0:50:91:0,91,1549 0/1:23,23:46:99:641,0,850 0/1:18,21:39:99:613,0,474 0/0:31,0:31:90:0,90,1350 0/1:15,13:28:99:368,0,591 0/0:28,0:28:75:0,75,1125 0/1:36,30:66:99:844,0,1379 0/1:32,35:67:99:1012,0,1218 0/1:26,40:66:99:1191,0,705 -chr16 80636220 rs12932528 A T 4857.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.408;DB;DP=457;ExcessHet=9.0714;FS=2.414;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.96;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.37;ReadPosRankSum=0.505;SOR=0.831;VQSLOD=8.64;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1593|-1||HGNC|23030|||||,T|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*2065T>A||3742/8159|||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.180142;gno_non_neuro_af_nfe=0.166176;gno_non_neuro_nhomalt_all=396;gno_non_neuro_nhomalt_nfe=214;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1221 0/1:13,20:33:99:597,0,308 0/0:41,0:41:99:0,101,1371 0/1:20,23:43:99:660,0,546 0/1:6,25:31:99:766,0,115 0/0:26,0:26:72:0,72,873 0/1:23,19:42:99:535,0,648 0/0:39,0:39:99:0,102,1420 0/1:32,33:65:99:911,0,907 0/1:23,21:44:99:568,0,632 0/1:28,30:58:99:838,0,789 -chr16 80636297 rs33943240 C G 4331.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.31;DB;DP=457;ExcessHet=9.0714;FS=4.295;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.96;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.62;ReadPosRankSum=-0.406;SOR=0.84;VQSLOD=8.59;culprit=MQRankSum;CSQ=G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||1516|-1||HGNC|23030|||||,G|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1988G>C||3665/8159|||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.219375;gno_non_neuro_af_nfe=0.169686;gno_non_neuro_nhomalt_all=618;gno_non_neuro_nhomalt_nfe=219;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1291 0/1:10,18:28:99:541,0,263 0/0:35,0:35:99:0,100,1201 0/1:14,25:39:99:711,0,359 0/1:14,22:36:99:657,0,368 0/0:29,0:29:87:0,87,958 0/1:21,21:42:99:544,0,534 0/0:35,0:35:99:0,99,1485 0/1:33,20:53:99:536,0,826 0/1:30,20:50:99:519,0,688 0/1:39,31:70:99:841,0,915 -chr16 80636940 rs74028318 G A 5437.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.786;DB;DP=495;ExcessHet=9.0714;FS=0.388;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.16;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=15.67;ReadPosRankSum=0.582;SOR=0.668;VQSLOD=7.82;culprit=MQRankSum;CSQ=A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|downstream_gene_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding|||||||||||873|-1||HGNC|23030|||||,A|3_prime_UTR_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding|7/7||ENST00000570137.2:c.*1345C>T||3022/8159|||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.170014;gno_non_neuro_af_nfe=0.156388;gno_non_neuro_nhomalt_all=356;gno_non_neuro_nhomalt_nfe=187;genic;highest_impact_order=36;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1485 0/1:13,18:31:99:530,0,359 0/0:37,0:37:99:0,105,1195 0/1:22,30:52:99:856,0,588 0/1:25,25:50:99:719,0,691 0/0:35,0:35:99:0,99,1311 0/1:10,27:37:99:801,0,212 0/0:41,0:41:99:0,109,1400 0/1:32,36:68:99:1025,0,903 0/1:29,19:48:99:491,0,814 0/1:26,35:61:99:1033,0,710 -chr16 80639833 rs74862994 T G 6796.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.055;DB;DP=482;ExcessHet=9.0714;FS=0.399;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=20.66;ReadPosRankSum=0.352;SOR=0.704;VQSLOD=22.13;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1390A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1390A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.222752;gno_non_neuro_af_nfe=0.17895;gno_non_neuro_nhomalt_all=592;gno_non_neuro_nhomalt_nfe=223;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,101,1485:. 0|1:16,18:34:99:0|1:80639833_T_G:705,0,649:80639833 0/0:38,0:38:99:.:.:0,100,1320:. 0|1:27,23:50:99:0|1:80639833_T_G:884,0,1064:80639833 0|1:19,19:38:99:0|1:80639833_T_G:741,0,1019:80639833 0/0:35,0:35:99:.:.:0,99,1232:. 0|1:22,23:45:99:0|1:80639833_T_G:942,0,1207:80639833 0/0:41,0:41:99:.:.:0,111,1665:. 0|1:31,31:62:99:0|1:80639833_T_G:1197,0,1475:80639833 0|1:14,30:44:99:0|1:80639833_T_G:1215,0,612:80639833 0|1:28,28:56:99:0|1:80639833_T_G:1130,0,1331:80639833 -chr16 80639836 rs77086080 G A 6787.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.752;DB;DP=483;ExcessHet=9.0714;FS=0.833;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=20.57;ReadPosRankSum=0.022;SOR=0.74;VQSLOD=22.1;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1393C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1393C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.190708;gno_non_neuro_af_nfe=0.178351;gno_non_neuro_nhomalt_all=423;gno_non_neuro_nhomalt_nfe=222;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,101,1485:. 0|1:16,18:34:99:0|1:80639833_T_G:705,0,649:80639833 0/0:38,0:38:99:.:.:0,100,1320:. 0|1:27,23:50:99:0|1:80639833_T_G:881,0,1096:80639833 0|1:19,19:38:99:0|1:80639833_T_G:738,0,1050:80639833 0/0:35,0:35:99:.:.:0,99,1232:. 0|1:21,24:45:99:0|1:80639833_T_G:945,0,1176:80639833 0/0:41,0:41:99:.:.:0,111,1665:. 0|1:31,30:61:99:0|1:80639833_T_G:1191,0,1529:80639833 0|1:15,30:45:99:0|1:80639833_T_G:1215,0,612:80639833 0|1:28,29:57:99:0|1:80639833_T_G:1130,0,1331:80639833 -chr16 80639841 rs4517811 G A 6724.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=479;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=20.63;ReadPosRankSum=0.07;SOR=0.693;VQSLOD=22.19;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||7/7|ENST00000562812.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||7/7|ENST00000563890.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||7/7|ENST00000566173.1:c.1366-1398C>T|||||||||-1||HGNC|23030|||||,A|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||6/6|ENST00000570137.2:c.1363-1398C>T|||||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.222883;gno_non_neuro_af_nfe=0.179213;gno_non_neuro_nhomalt_all=593;gno_non_neuro_nhomalt_nfe=224;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,101,1485:. 0|1:17,18:35:99:0|1:80639833_T_G:705,0,649:80639833 0/0:38,0:38:99:.:.:0,100,1320:. 0|1:28,23:51:99:0|1:80639833_T_G:881,0,1096:80639833 0|1:19,18:37:99:0|1:80639833_T_G:696,0,1053:80639833 0/0:35,0:35:99:.:.:0,99,1232:. 0|1:20,22:42:99:0|1:80639833_T_G:906,0,1137:80639833 0/0:41,0:41:99:.:.:0,111,1665:. 0|1:32,30:62:99:0|1:80639833_T_G:1175,0,1498:80639833 0|1:15,30:45:99:0|1:80639833_T_G:1246,0,609:80639833 0|1:28,26:54:99:0|1:80639833_T_G:1133,0,1288:80639833 -chr16 80834946 rs11150314 T G 4455.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.806;DB;DP=484;ExcessHet=9.0714;FS=2.88;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.07;ReadPosRankSum=0.217;SOR=0.863;VQSLOD=23.42;culprit=MQRankSum;CSQ=G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000562812|protein_coding||1/7|ENST00000562812.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000563890|protein_coding||1/7|ENST00000563890.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000566173|protein_coding||1/7|ENST00000566173.1:c.24+3101A>C|||||||||-1||HGNC|23030|||||,G|intron_variant|MODIFIER|CDYL2|ENSG00000166446|Transcript|ENST00000570137|protein_coding||1/6|ENST00000570137.2:c.24+3101A>C|||||||||-1||HGNC|23030|YES|CCDS32493.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.283008;gno_non_neuro_af_nfe=0.266613;gno_non_neuro_nhomalt_all=871;gno_non_neuro_nhomalt_nfe=480;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,102,1320 0/1:22,17:39:99:429,0,628 0/0:34,0:34:99:0,99,1141 0/1:34,22:56:99:566,0,962 0/1:14,16:30:99:466,0,376 0/0:36,0:36:99:0,100,1205 0/1:17,11:28:99:277,0,462 0/0:34,0:34:99:0,99,1162 0/1:26,39:65:99:1125,0,709 0/1:26,25:51:99:689,0,750 0/1:37,35:72:99:921,0,1050 -chr16 81393010 rs71146005 G GT 1074.52 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.16;DB;DP=342;ExcessHet=9.0714;FS=15.728;InbreedingCoeff=-0.4377;MLEAC=7;MLEAF=0.318;MQ=59.94;MQRankSum=0;QD=8.46;ReadPosRankSum=0.491;SOR=1.837;VQSLOD=5.1;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|GAN|ENSG00000261609|Transcript|ENST00000568107|protein_coding||5/10|ENST00000568107.2:c.973+1491dup|||||||||1||HGNC|4137|YES|CCDS10935.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.433732;gno_non_neuro_af_nfe=0.491475;gno_non_neuro_nhomalt_all=1376;gno_non_neuro_nhomalt_nfe=1103;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:36,0:36:48:0,48,1021 0/1:7,9:16:99:167,0,103 0/0:40,0:40:96:0,96,1281 0/1:4,9:13:36:158,0,36 0/1:14,8:22:99:101,0,236 0/0:35,0:35:41:0,41,958 0/1:18,10:28:99:125,0,716 0/0:41,0:41:54:0,54,1216 0/1:2,9:11:10:163,0,10 0/1:5,8:16:65:152,0,65 0/1:10,14:24:99:226,0,125 -chr16 82152710 rs11639926 G T 5032.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.398;DB;DP=501;ExcessHet=9.0714;FS=9.547;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.595;SOR=0.405;VQSLOD=23.96;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|CTD-2588J6.1|ENSG00000260161|Transcript|ENST00000566728|processed_pseudogene|||||||||||1533|-1||Clone_based_vega_gene||YES||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+20484C>A|||||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.170261;gno_non_neuro_af_nfe=0.200132;gno_non_neuro_nhomalt_all=303;gno_non_neuro_nhomalt_nfe=265;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:34,0:34:99:0,99,1206 0/1:22,22:44:99:598,0,629 0/0:39,0:39:99:0,103,1256 0/1:24,30:54:99:855,0,637 0/1:20,21:41:99:607,0,571 0/0:32,0:32:93:0,93,1395 0/1:18,18:36:99:473,0,508 0/0:37,0:37:99:0,102,1342 0/1:33,40:73:99:1136,0,916 0/1:27,29:56:99:793,0,768 0/1:31,23:54:99:588,0,916 -chr16 82161091 rs35999878 TA T 5062.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=477;ExcessHet=9.0714;FS=8.803;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.51;ReadPosRankSum=-0.067;SOR=0.888;VQSLOD=9.41;culprit=MQRankSum;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-510J16.5|ENSG00000261235|Transcript|ENST00000567021|antisense||1/3|ENST00000567021.1:n.43+12102del|||||||||-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.22923;gno_non_neuro_af_nfe=0.284585;gno_non_neuro_nhomalt_all=309;gno_non_neuro_nhomalt_nfe=271;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:33,0:33:96:.:.:0,96,1440:. 0|1:14,18:32:99:0|1:82161091_TA_T:601,0,463:82161091 0/0:39,0:39:99:.:.:0,100,1315:. 0|1:24,22:46:99:0|1:82161091_TA_T:730,0,826:82161091 0|1:31,21:52:99:0|1:82161091_TA_T:672,0,1094:82161091 0/0:29,0:29:81:.:.:0,81,1215:. 0|1:24,15:39:99:0|1:82161091_TA_T:459,0,836:82161091 0/0:25,0:25:60:.:.:0,60,900:. 0|1:26,21:47:99:0|1:82161091_TA_T:666,0,909:82161091 0|1:33,31:64:99:0|1:82161091_TA_T:1024,0,1132:82161091 0|1:40,29:69:99:0|1:82161091_TA_T:928,0,1401:82161091 -chr16 82294753 rs35812977 A G 3704.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.442;DB;DP=455;ExcessHet=9.0714;FS=7.721;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.15;ReadPosRankSum=0.508;SOR=0.425;VQSLOD=23.56;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.0416353;gno_non_neuro_af_nfe=0.0542824;gno_non_neuro_nhomalt_all=25;gno_non_neuro_nhomalt_nfe=22;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,101,1351 0/1:14,13:27:99:336,0,406 0/0:39,0:39:99:0,105,1316 0/1:17,24:41:99:661,0,458 0/1:20,22:42:99:618,0,569 0/0:34,0:34:93:0,93,1395 0/1:14,22:36:99:612,0,379 0/0:36,0:36:99:0,99,1174 0/1:27,18:45:99:410,0,803 0/1:27,26:53:99:574,0,759 0/1:37,24:61:99:511,0,1078 -chr19 52133734 rs62115014 G A 2625.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.996;DB;DP=358;ExcessHet=9.0714;FS=22.608;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=48.84;MQRankSum=1.86;NEGATIVE_TRAIN_SITE;QD=10.89;ReadPosRankSum=0.438;SOR=1.647;VQSLOD=-5.591;culprit=MQ;CSQ=A|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-845C>T|||||||||-1||HGNC|10874|||||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-265C>T|||||||||-1||Uniprot_gn|10874|YES||||,A|5_prime_UTR_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding|2/10||ENST00000534261.2:c.-146C>T||255/2356|||||||-1||HGNC|10874||CCDS33088.1|||,A|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||146|-1||HGNC|10874|YES|CCDS33088.1|||,A|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-845C>T|||||||||-1||Uniprot_gn|10874|||||;cadd_phred=-1;gno_non_neuro_af_all=0.298587;gno_non_neuro_af_nfe=0.278243;gno_non_neuro_nhomalt_all=828;gno_non_neuro_nhomalt_nfe=446;genic;highest_impact_order=35;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,105,1305 0/1:23,15:38:99:406,0,639 0/0:32,0:32:90:0,90,1350 0/1:13,15:28:99:437,0,352 0/1:25,14:39:99:363,0,730 0/0:31,0:31:90:0,90,1037 0/1:22,15:37:99:401,0,568 0/0:15,0:15:45:0,45,501 0/1:20,8:28:99:191,0,590 0/1:18,18:36:99:501,0,495 0/1:21,14:35:99:344,0,532 -chr19 52134334 . TA T 1565.46 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.496;DP=346;ExcessHet=9.0714;FS=9.467;InbreedingCoeff=-0.5172;MLEAC=7;MLEAF=0.318;MQ=59.87;MQRankSum=0;QD=9.91;ReadPosRankSum=-0.266;SOR=0.35;VQSLOD=5.73;culprit=MQRankSum;CSQ=-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-1446del|||||||||-1||HGNC|10874|||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-866del|||||||||-1||Uniprot_gn|10874|YES||||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-416del|||||||||-1||HGNC|10874||CCDS33088.1|||,-|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||747|-1||HGNC|10874|YES|CCDS33088.1|||,-|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-1446del|||||||||-1||Uniprot_gn|10874|||||;cadd_phred=-1;gno_non_neuro_af_all=0.300644;gno_non_neuro_af_nfe=0.330881;gno_non_neuro_nhomalt_all=704;gno_non_neuro_nhomalt_nfe=588;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:90:0,90,1350 0/1:5,14:19:53:265,0,53 0/0:41,0:41:99:0,107,1121 0/1:13,15:28:99:287,0,188 0/1:10,14:26:99:234,0,164 0/0:35,0:35:90:0,90,1090 0/1:7,9:16:99:160,0,106 0/0:11,0:11:0:0,0,293 0/1:15,13:30:99:228,0,242 0/1:14,11:25:99:180,0,208 0/1:5,13:18:48:225,0,48 -chr19 52135776 rs35970457 G T 4332.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.69;DB;DP=418;ExcessHet=9.0714;FS=6.217;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.94;ReadPosRankSum=0.448;SOR=0.453;VQSLOD=23.53;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000222107|protein_coding||2/8|ENST00000222107.4:c.422-2887C>A|||||||||-1||HGNC|10874|||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000429354|protein_coding||1/8|ENST00000429354.3:c.38-2307C>A|||||||||-1||Uniprot_gn|10874|YES||||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000534261|protein_coding||1/9|ENST00000534261.2:c.-331-1857C>A|||||||||-1||HGNC|10874||CCDS33088.1|||,T|upstream_gene_variant|MODIFIER|SIGLEC5|ENSG00000105501|Transcript|ENST00000570106|protein_coding|||||||||||2188|-1||HGNC|10874|YES|CCDS33088.1|||,T|intron_variant|MODIFIER|SIGLEC5|ENSG00000268500|Transcript|ENST00000599649|protein_coding||2/8|ENST00000599649.1:c.422-2887C>A|||||||||-1||Uniprot_gn|10874|||||;cadd_phred=-1;gno_non_neuro_af_all=0.291102;gno_non_neuro_af_nfe=0.327437;gno_non_neuro_nhomalt_all=1319;gno_non_neuro_nhomalt_nfe=1031;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1220 0/1:18,11:29:99:295,0,498 0/0:36,0:36:59:0,59,1072 0/1:26,19:45:99:497,0,654 0/1:16,22:38:99:616,0,432 0/0:36,0:36:94:0,94,1142 0/1:11,18:29:99:539,0,270 0/0:16,0:16:48:0,48,526 0/1:16,33:49:99:970,0,299 0/1:18,21:39:99:593,0,393 0/1:31,30:61:99:840,0,669 -chr19 52250589 rs7253355 G A 3852.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.35;DB;DP=445;ExcessHet=9.0714;FS=0.884;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.98;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=13.19;ReadPosRankSum=0.264;SOR=0.751;VQSLOD=8.56;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-331C>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-331C>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4690|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-331C>T|||||||||-1|cds_end_NF|HGNC|3826|||||;cadd_phred=-1;gno_non_neuro_af_all=0.248148;gno_non_neuro_af_nfe=0.229188;gno_non_neuro_nhomalt_all=668;gno_non_neuro_nhomalt_nfe=367;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:48,0:48:99:0,116,1625 0/1:10,19:29:99:563,0,260 0/0:35,0:35:70:0,70,1107 0/1:21,22:43:99:616,0,536 0/1:31,13:44:99:320,0,850 0/0:29,0:29:81:0,81,1215 0/1:13,10:23:99:269,0,348 0/0:37,0:37:99:0,101,1240 0/1:24,18:42:99:454,0,618 0/1:19,26:45:99:768,0,455 0/1:34,32:66:99:880,0,769 -chr19 52250888 rs113978889 G GATTCATGAATAC 7078.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.199;DB;DP=466;ExcessHet=9.0714;FS=0.416;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=23.13;ReadPosRankSum=-0.59;SOR=0.74;VQSLOD=8.83;culprit=MQRankSum;CSQ=ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826||CCDS12839.1|||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,ATTCATGAATAC|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4390|1|cds_end_NF|HGNC|3827|||||,ATTCATGAATAC|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-631_-11-630insGTATTCATGAAT|||||||||-1|cds_end_NF|HGNC|3826|||||;cadd_phred=-1;gno_non_neuro_af_all=0.242757;gno_non_neuro_af_nfe=0.225191;gno_non_neuro_nhomalt_all=577;gno_non_neuro_nhomalt_nfe=313;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,105,1524:. 0|1:14,15:29:99:0|1:52250888_G_GATTCATGAATAC:627,0,2162:52250888 0/0:35,0:35:93:.:.:0,93,1182:. 0|1:19,22:41:99:0|1:52250888_G_GATTCATGAATAC:902,0,2920:52250888 0|1:24,15:39:99:0|1:52250888_G_GATTCATGAATAC:639,0,3998:52250888 0/0:30,0:30:81:.:.:0,81,1215:. 0|1:14,20:34:99:0|1:52250888_G_GATTCATGAATAC:839,0,2184:52250888 0/0:43,0:43:99:.:.:0,101,1445:. 0|1:17,36:53:99:0|1:52250888_G_GATTCATGAATAC:1499,0,953:52250888 0|1:21,25:46:99:0|1:52250888_G_GATTCATGAATAC:1084,0,3342:52250888 0|1:32,32:64:99:0|1:52250888_G_GATTCATGAATAC:1506,0,5140:52250888 -chr19 52250892 rs12980168 T A 6593.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=471;ExcessHet=9.0714;FS=0.848;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.03;MQRankSum=0;QD=20.67;ReadPosRankSum=-0.977;SOR=0.628;VQSLOD=6.95;culprit=MQRankSum;CSQ=A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000304748|protein_coding||1/1|ENST00000304748.4:c.-11-634A>T|||||||||-1||HGNC|3826||CCDS12839.1|||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000594900|protein_coding||2/2|ENST00000594900.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000595042|protein_coding||2/2|ENST00000595042.1:c.-11-634A>T|||||||||-1||HGNC|3826|YES|CCDS12839.1|||,A|upstream_gene_variant|MODIFIER|FPR2|ENSG00000171049|Transcript|ENST00000600258|protein_coding|||||||||||4387|1|cds_end_NF|HGNC|3827|||||,A|intron_variant|MODIFIER|FPR1|ENSG00000171051|Transcript|ENST00000600815|protein_coding||1/1|ENST00000600815.1:c.-11-634A>T|||||||||-1|cds_end_NF|HGNC|3826|||||;cadd_phred=-1;gno_non_neuro_af_all=0.243128;gno_non_neuro_af_nfe=0.225295;gno_non_neuro_nhomalt_all=578;gno_non_neuro_nhomalt_nfe=313;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,105,1524:. 0|1:14,16:30:99:0|1:52250888_G_GATTCATGAATAC:657,0,2159:52250888 0/0:36,0:36:99:.:.:0,99,1485:. 0|1:22,23:45:99:0|1:52250888_G_GATTCATGAATAC:899,0,2951:52250888 0|1:25,17:42:99:0|1:52250888_G_GATTCATGAATAC:639,0,3998:52250888 0/0:30,0:30:81:.:.:0,81,1215:. 0|1:14,20:34:99:0|1:52250888_G_GATTCATGAATAC:798,0,2187:52250888 0/0:43,0:43:99:.:.:0,101,1445:. 0|1:20,34:54:99:0|1:52250888_G_GATTCATGAATAC:1367,0,1025:52250888 0|1:22,22:44:99:0|1:52250888_G_GATTCATGAATAC:829,0,3392:52250888 0|1:33,37:70:99:0|1:52250888_G_GATTCATGAATAC:1422,0,5146:52250888 -chr19 53546001 rs11456354 C CT 3168.1 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=461;ExcessHet=9.3779;FS=11.346;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.05;MQRankSum=0;QD=10.25;ReadPosRankSum=-0.105;SOR=0.731;VQSLOD=6.98;culprit=MQRankSum;CSQ=T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000594516|processed_transcript|||||||||||4865|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ZNF702P|ENSG00000242779|Transcript|ENST00000600425|processed_transcript|||||||||||4850|-1||HGNC|25775|||||,T|upstream_gene_variant|MODIFIER|ERVV-2|ENSG00000268964|Transcript|ENST00000601417|protein_coding|||||||||||1989|1||HGNC|39051|YES|CCDS59420.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.34934;gno_non_neuro_af_nfe=0.373508;gno_non_neuro_nhomalt_all=859;gno_non_neuro_nhomalt_nfe=628;highest_impact_order=51;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:36,0:36:99:.:.:0,102,1530:. 0|1:20,14:34:99:0|1:53546001_C_CT:286,0,435:53546001 0|0:11,0:20:99:0|1:53546001_C_CTT:252,286,647:53546001 1/0:7,12:31:88:.:.:453,100,188:. 0/1:30,15:45:99:.:.:256,0,619:. 0/0:11,0:22:99:.:.:303,336,672:. 0/1:33,10:43:99:.:.:125,0,706:. 0/0:13,0:27:99:.:.:403,442,867:. 0/1:29,8:40:90:.:.:90,0,687:. 0/1:12,16:29:99:.:.:327,0,201:. 1/0:1,8:28:99:.:.:705,371,320:. -chr20 25742657 rs112655215 TA T 1518.7 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=0.872;DB;DP=554;ExcessHet=9.0714;FS=9.573;InbreedingCoeff=-0.4985;MLEAC=7;MLEAF=0.318;MQ=56.51;MQRankSum=-6.102;NEGATIVE_TRAIN_SITE;QD=4.1;ReadPosRankSum=1.54;SOR=1.37;VQSLOD=-2.626;culprit=MQ;CSQ=-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1444|-1||HGNC|34503|||||,-|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1444|-1||HGNC|34503|||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:39,0:39:96:.:.:0,96,1440:. 0|1:36,3:39:18:0|1:25742657_TA_T:18,0,2465:25742657 0/0:42,0:42:99:.:.:0,103,1379:. 0|1:32,7:39:99:0|1:25742657_TA_T:198,0,1857:25742657 0|1:32,5:37:99:0|1:25742657_TA_T:132,0,1825:25742657 0|0:29,2:31:3:0|1:25742657_TA_T:0,3,1315:25742657 0|1:31,5:36:99:0|1:25742657_TA_T:117,0,1606:25742657 0/0:26,0:26:70:.:.:0,70,904:. 0|1:63,14:77:99:0|1:25742657_TA_T:391,0,2594:25742657 0|1:54,10:64:99:0|1:25742657_TA_T:250,0,2242:25742657 0|1:63,15:78:99:0|1:25742657_TA_T:428,0,3582:25742657 -chr20 25742669 rs62213491 G A 1466.43 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.104;DB;DP=548;ExcessHet=9.0714;FS=14.421;InbreedingCoeff=-0.5141;MLEAC=7;MLEAF=0.318;MQ=56.4;MQRankSum=-6.102;QD=4.03;ReadPosRankSum=0.242;SOR=1.367;VQSLOD=-2.682;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000376404|protein_coding|||||||||||1433|-1||HGNC|34503|||||,A|downstream_gene_variant|MODIFIER|FAM182B|ENSG00000175170|Transcript|ENST00000478164|processed_transcript|||||||||||1433|-1||HGNC|34503|||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:36,0:36:39:.:.:0,39,1092:. 0|1:36,3:39:15:0|1:25742657_TA_T:15,0,2484:25742657 0/0:41,0:41:54:.:.:0,54,1256:. 0|1:33,8:41:99:0|1:25742657_TA_T:221,0,1880:25742657 0|1:35,7:42:99:0|1:25742657_TA_T:153,0,1881:25742657 0|0:28,2:30:0:0|1:25742657_TA_T:0,0,1274:25742657 0|1:29,5:34:99:0|1:25742657_TA_T:123,0,1520:25742657 0/0:36,0:36:39:.:.:0,39,1113:. 0|1:61,13:74:99:0|1:25742657_TA_T:359,0,2488:25742657 0|1:54,9:63:99:0|1:25742657_TA_T:209,0,2253:25742657 0|1:57,14:71:99:0|1:25742657_TA_T:400,0,3445:25742657 -chr20 52482965 rs57319922 ATT A 3524.69 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.89;DB;DP=405;ExcessHet=0.5742;FS=0;InbreedingCoeff=0.3714;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=15.88;ReadPosRankSum=0.366;SOR=0.707;VQSLOD=8.98;culprit=MQRankSum;CSQ=-|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:43:86:86,197,1635 0/1:5,9:24:99:538,289,440 0/0:41,0:41:89:0,89,1346 0/1:6,8:23:12:684,468,764 0/1:15,10:25:99:227,0,386 0/0:41,0:41:99:0,111,1320 0/1:7,9:23:60:307,60,216 0/0:11,7:31:99:584,410,703 1/0:1,14:16:20:476,91,76 1/0:4,5:11:54:198,69,144 1/0:4,7:28:62:485,320,476 -chr20 54033324 rs34543864;rs67863628 C CT 3775.1 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.348;DB;DP=258;ExcessHet=2.9436;FS=29.934;InbreedingCoeff=-0.1273;MLEAC=6;MLEAF=0.273;MQ=57.8;MQRankSum=0;QD=29.73;ReadPosRankSum=-0.589;SOR=0.036;VQSLOD=0.33;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|RP5-1010E17.2|ENSG00000224008|Transcript|ENST00000433766|lincRNA|||||||||||3549|-1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:3,0:26:99:951,966,1137 0/1:0,7:14:99:388,272,251 0/0:8,0:17:99:354,378,933 0/1:0,7:14:99:368,252,231 0/1:0,5:24:98:865,782,767 0/0:9,0:10:2:0,14,161 0/1:3,4:9:31:83,0,31 0/0:4,0:13:99:364,376,470 1/0:0,1:3:14:144,62,44 0/1:1,1:9:1:284,271,284 0/1:2,1:4:9:9,0,15 -chr20 54066953 . G GT 2623.89 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.566;DP=424;ExcessHet=6.4503;FS=6.589;InbreedingCoeff=-0.3162;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;QD=12.32;ReadPosRankSum=-0.02;SOR=1.008;VQSLOD=8.23;culprit=MQRankSum;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|RP5-1010E17.1|ENSG00000235166|Transcript|ENST00000416190|lincRNA||4/7|ENST00000416190.1:n.685-1124_685-1123insT|||||||||1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.536377;gno_non_neuro_af_nfe=0.607916;gno_non_neuro_nhomalt_all=2722;gno_non_neuro_nhomalt_nfe=2223;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:43,0:43:96:0,96,1440 0/1:8,6:14:99:195,0,319 0/0:38,0:38:87:0,87,1305 0/1:11,14:25:99:479,0,420 0/1:22,17:39:99:523,0,853 0/0:39,0:39:96:0,96,1440 1/0:0,10:21:99:602,323,406 0/0:11,0:28:99:610,588,928 0/1:27,11:38:99:239,0,1298 0/1:6,11:17:99:372,0,189 0/1:15,16:31:99:508,0,570 -chr20 56003327 rs6064549 T G 2573.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.935;DB;DP=363;ExcessHet=9.0714;FS=3.606;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60.27;MQRankSum=0;QD=13.91;ReadPosRankSum=0.759;SOR=0.47;VQSLOD=5;culprit=MQRankSum;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.26186;gno_non_neuro_af_nfe=0.310772;gno_non_neuro_nhomalt_all=656;gno_non_neuro_nhomalt_nfe=538;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:44,0:44:99:.:.:0,99,1485:. 0/1:15,10:25:99:.:.:345,0,514:. 0/0:41,0:41:99:.:.:0,99,1274:. 0|1:14,14:28:99:0|1:56003327_T_G:525,0,826:56003327 0/1:8,14:22:99:.:.:572,0,299:. 0/0:27,0:27:72:.:.:0,72,1080:. 0/1:13,12:25:99:.:.:411,0,500:. 0/0:53,0:53:99:.:.:0,108,1646:. 0/1:6,17:23:56:.:.:377,0,56:. 0/1:17,5:22:83:.:.:83,0,583:. 0/1:26,14:40:99:.:.:278,0,730:. -chr20 57159924 rs138169217;rs58239093 TTTCC T 3495.38 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=377;ExcessHet=9.0714;FS=1.121;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.65;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=18.3;ReadPosRankSum=0.094;SOR=0.604;VQSLOD=6.39;culprit=MQRankSum;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-33855_944-33852del|||||||||1||HGNC|27152|||||;cadd_phred=-1;gno_non_neuro_af_all=0.417144;gno_non_neuro_af_nfe=0.450964;gno_non_neuro_nhomalt_all=1789;gno_non_neuro_nhomalt_nfe=1316;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,100,1326 0/1:9,8:17:99:298,0,467 0/0:42,0:42:99:0,100,1244 0/1:13,12:25:99:445,0,512 0/1:13,23:36:99:927,0,639 0/0:37,0:37:81:0,81,995 0/1:16,9:25:99:317,0,670 0/0:39,0:39:99:0,108,1620 0/1:19,16:35:99:615,0,945 0/1:17,10:27:99:369,0,895 0/1:11,15:26:99:542,0,408 -chr20 57164080 rs4812020 G A 4106.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.066;DB;DP=484;ExcessHet=9.0714;FS=3.527;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.29;ReadPosRankSum=0.658;SOR=0.769;VQSLOD=23.65;culprit=MQRankSum;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|APCDD1L-AS1|ENSG00000231290|Transcript|ENST00000427140|lincRNA||6/6|ENST00000427140.1:n.944-29716G>A|||||||||1||HGNC|27152|||||;cadd_phred=-1;gno_non_neuro_af_all=0.480499;gno_non_neuro_af_nfe=0.492061;gno_non_neuro_nhomalt_all=2472;gno_non_neuro_nhomalt_nfe=1647;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,99,1459 0/1:25,19:44:99:529,0,671 0/0:35,0:35:99:0,105,1167 0/1:22,17:39:99:444,0,648 0/1:24,23:47:99:649,0,628 0/0:36,0:36:99:0,99,1191 0/1:18,22:40:99:605,0,481 0/0:40,0:40:99:0,108,1391 0/1:35,18:53:99:456,0,1046 0/1:24,26:50:99:696,0,684 0/1:33,28:61:99:745,0,964 -chr20 57246491 rs35720492 TGG * 3220.93 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=431;ExcessHet=9.3779;FS=7.165;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=59.75;MQRankSum=0;QD=9.47;ReadPosRankSum=-0.044;SOR=1.03;VQSLOD=4.91;culprit=MQRankSum;cadd_phred=-1;gno_non_neuro_af_all=0.372515;gno_non_neuro_af_nfe=0.403123;gno_non_neuro_nhomalt_all=1386;gno_non_neuro_nhomalt_nfe=1055;highest_impact_order=2147483646;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0|0:18,0:37:99:0|1:57246480_T_TTTA:744,798,2276:57246480 0/1:18,7:25:99:.:.:321,0,1225:. 0|0:16,0:35:99:0|1:57246480_T_TTTA:728,779,1790:57246480 0|1:14,16:30:99:0|1:57246478_C_CT:672,0,537:57246478 0|1:23,26:49:99:0|1:57246478_C_CT:1023,0,1776:57246478 0|0:14,0:29:99:0|1:57246480_T_TTTA:585,630,1785:57246480 0/1:0,17:27:99:.:.:1368,397,326:. 0/0:40,0:40:99:.:.:0,107,1340:. 0/1:32,14:49:99:.:.:742,0,1316:. 0/1:0,8:26:99:.:.:1783,788,713:. 0/1:24,12:37:99:.:.:818,0,966:. -chr20 57311528 rs60524735;rs71181980 CA C 1771.2 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=192;ExcessHet=4.4261;FS=9.388;InbreedingCoeff=-0.221;MLEAC=7;MLEAF=0.318;MQ=60.31;MQRankSum=0;QD=20.36;ReadPosRankSum=0;SOR=0.077;VQSLOD=5.11;culprit=MQRankSum;CSQ=-|downstream_gene_variant|MODIFIER|PIEZO1P2|ENSG00000237121|Transcript|ENST00000416241|unprocessed_pseudogene|||||||||||4059|-1||HGNC|42861|YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.387299;gno_non_neuro_af_nfe=0.38905;gno_non_neuro_nhomalt_all=271;gno_non_neuro_nhomalt_nfe=190;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:1,0:4:18:74,77,104 0/1:0,6:12:99:204,111,123 0/0:6,0:10:88:88,128,519 0/1:0,6:9:85:182,85,91 0/1:0,10:17:99:342,191,220 0/0:4,0:8:76:95,112,253 0/1:0,6:10:99:255,171,212 0/0:0,0:9:30:290,260,257 0/1:0,3:4:34:79,34,47 0/1:1,4:6:27:46,0,27 0/1:0,3:5:38:102,44,38 -chr21 9830249 rs75884386 G A 7055.8 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.94;DB;DP=1399;ExcessHet=9.0714;FS=1.903;InbreedingCoeff=-0.6299;MLEAC=8;MLEAF=0.364;MQ=57.17;MQRankSum=0.828;NEGATIVE_TRAIN_SITE;QD=8;ReadPosRankSum=-0.978;SOR=0.653;VQSLOD=-2.57;culprit=MQ;CSQ=A|downstream_gene_variant|MODIFIER|MIR3687|ENSG00000264063|Transcript|ENST00000577708|miRNA|||||||||||3986|1||HGNC|38946|YES||||,A|downstream_gene_variant|MODIFIER|MIR3648|ENSG00000264462|Transcript|ENST00000581792|miRNA|||||||||||4238|1||HGNC|38941|YES||||;cadd_phred=-1;gno_non_neuro_af_all=-1;gno_non_neuro_af_nfe=-1;gno_non_neuro_nhomalt_all=-1;gno_non_neuro_nhomalt_nfe=-1;highest_impact_order=53;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:98,0:98:0:0,0,2292 0/1:56,57:113:99:1603,0,1446 0/0:119,0:119:0:0,0,2389 0/1:60,54:114:99:1480,0,1715 0/1:60,54:114:99:1411,0,1733 0/0:117,0:117:0:0,0,2327 0/1:39,42:81:99:1107,0,1033 0/0:90,8:98:26:0,26,2928 0/1:140,53:193:99:1237,0,3794 0/1:75,14:89:99:167,0,2254 0/1:161,17:178:55:55,0,4528 -chrX 134937170 rs200921509 G GAAAAGA 3549.4 VQSRTrancheINDEL99.00to99.90 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.14;DB;DP=224;ExcessHet=9.0714;FS=0;InbreedingCoeff=-0.4671;MLEAC=7;MLEAF=0.318;MQ=25.64;MQRankSum=0.134;QD=24.15;ReadPosRankSum=0.845;SOR=1.041;VQSLOD=-0.504;culprit=MQ;CSQ=AAAAGA|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.170-6284_170-6279dup|||||||||-1||HGNC|33269|||||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000434966|protein_coding|||||||||||435|-1||HGNC|33269||CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000487941|protein_coding|||||||||||435|-1||HGNC|33269|YES|CCDS35405.1|||,AAAAGA|upstream_gene_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000494421|protein_coding|||||||||||620|-1||HGNC|33269||CCDS35405.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.483591;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.479371;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=32;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=19;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:15,0:15:45:0,45,501 0/1:12,9:21:99:342,0,490 0/0:9,0:9:27:0,27,272 0/1:10,3:13:96:96,0,447 0/1:2,8:10:99:359,0,114 0/0:25,0:25:40:0,40,749 0/1:16,9:25:99:330,0,832 0/0:9,0:9:27:0,27,282 0/1:11,37:50:99:1641,0,327 0/1:4,3:7:99:114,0,242 0/1:9,14:25:99:685,0,312 -chrX 134948600 rs28496014 C T 5864.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.389;DB;DP=504;ExcessHet=9.0714;FS=193.058;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=50.9;MQRankSum=-5.098;QD=15.19;ReadPosRankSum=-2.875;SOR=4.094;VQSLOD=-257.2;culprit=FS;CSQ=T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1478G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-445G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-445G>A|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.420312;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.404793;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:32,30:62:99:0|1:134948600_C_T:1205,0,1319:134948600 0/0:19,0:19:54:.:.:0,54,810:. 0|1:43,30:73:99:0|1:134948600_C_T:1234,0,1910:134948600 0|1:17,36:53:99:0|1:134948600_C_T:1476,0,602:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:38,33:71:99:0|1:134948600_C_T:1292,0,1630:134948600 0/0:23,0:23:66:.:.:0,66,759:. 0|1:47,9:56:99:0|1:134948600_C_T:360,0,1934:134948600 0|1:26,2:28:90:0|1:134948600_C_T:90,0,1016:134948600 0|1:37,6:43:99:0|1:134948600_C_T:225,0,1478:134948600 -chrX 134948607 rs28548436 G A 8264.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.104;DB;DP=548;ExcessHet=9.0714;FS=106.681;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=50.71;MQRankSum=-5.313;QD=19.31;ReadPosRankSum=-3.049;SOR=4.047;VQSLOD=-85.24;culprit=ReadPosRankSum;CSQ=A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1471C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-452C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-452C>T|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.421811;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.406186;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:33,36:69:99:0|1:134948600_C_T:1451,0,1385:134948600 0/0:20,0:20:54:.:.:0,54,810:. 0|1:46,36:82:99:0|1:134948600_C_T:1483,0,1950:134948600 0|1:18,39:57:99:0|1:134948600_C_T:1696,0,629:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:36,33:69:99:0|1:134948600_C_T:1410,0,1644:134948600 0/0:24,0:24:72:.:.:0,72,774:. 0|1:46,24:70:99:0|1:134948600_C_T:1202,0,1877:134948600 0|1:22,9:31:99:0|1:134948600_C_T:390,0,951:134948600 0|1:33,17:50:99:0|1:134948600_C_T:650,0,1405:134948600 -chrX 134948616 rs80141830 C G 10797.4 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.522;DB;DP=613;ExcessHet=9.0714;FS=100.79;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=48.97;MQRankSum=-6.059;QD=21.77;ReadPosRankSum=-2.647;SOR=3.591;VQSLOD=-77.59;culprit=FS;CSQ=G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1462G>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-461G>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-461G>C|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.429463;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.416219;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:35,43:78:99:0|1:134948600_C_T:1700,0,1409:134948600 0/0:19,0:19:57:.:.:0,57,640:. 0|1:45,41:86:99:0|1:134948600_C_T:1625,0,1909:134948600 0|1:19,46:65:99:0|1:134948600_C_T:1913,0,698:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:38,40:78:99:0|1:134948600_C_T:1562,0,1655:134948600 0/0:22,0:22:63:.:.:0,63,735:. 0|1:46,55:101:99:0|1:134948600_C_T:2450,0,1955:134948600 0|1:19,14:33:99:0|1:134948600_C_T:570,0,795:134948600 0|1:31,24:55:99:0|1:134948600_C_T:995,0,1265:134948600 -chrX 134948621 rs76502734 G A 12312.4 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.303;DB;DP=648;ExcessHet=9.0714;FS=94.1;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=47.7;MQRankSum=-6.004;QD=23.19;ReadPosRankSum=-1.462;SOR=3.563;VQSLOD=-69.37;culprit=FS;CSQ=A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1457C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-466C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-466C>T|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.432844;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.420593;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:33,45:78:99:0|1:134948600_C_T:1829,0,1358:134948600 0/0:19,0:19:51:.:.:0,51,765:. 0|1:47,44:91:99:0|1:134948600_C_T:1745,0,1984:134948600 0|1:21,52:73:99:0|1:134948600_C_T:2246,0,716:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:37,42:79:99:0|1:134948600_C_T:1694,0,1562:134948600 0/0:22,0:22:63:.:.:0,63,735:. 0|1:48,66:114:99:0|1:134948600_C_T:2912,0,1922:134948600 0|1:19,16:35:99:0|1:134948600_C_T:699,0,744:134948600 0|1:32,29:61:99:0|1:134948600_C_T:1205,0,1250:134948600 -chrX 134948627 rs28564164 G T 13551.4 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=689;ExcessHet=9.0714;FS=77.771;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=46.64;MQRankSum=-6.154;QD=23.69;ReadPosRankSum=-0.588;SOR=3.175;VQSLOD=-49.84;culprit=FS;CSQ=T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1451C>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-472C>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-472C>A|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.433457;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.422021;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:34,46:80:99:0|1:134948600_C_T:1871,0,1355:134948600 0/0:19,0:19:57:.:.:0,57,640:. 0|1:49,48:97:99:0|1:134948600_C_T:1868,0,2017:134948600 0|1:20,55:75:99:0|1:134948600_C_T:2246,0,716:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:38,43:81:99:0|1:134948600_C_T:1691,0,1604:134948600 0/0:22,0:22:63:.:.:0,63,735:. 0|1:53,81:134:99:0|1:134948600_C_T:3488,0,2048:134948600 0|1:18,22:40:99:0|1:134948600_C_T:990,0,765:134948600 0|1:30,35:65:99:0|1:134948600_C_T:1415,0,1235:134948600 -chrX 134948631 rs200670901 T C 14512.4 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0;DB;DP=714;ExcessHet=9.0714;FS=73.518;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=45.91;MQRankSum=-6.184;QD=24.31;ReadPosRankSum=0.148;SOR=3.066;VQSLOD=-45.68;culprit=MQ;CSQ=C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1447A>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-476A>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-476A>G|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.434103;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.42281;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:33,47:80:99:0|1:134948600_C_T:1900,0,1352:134948600 0/0:19,0:19:57:.:.:0,57,640:. 0|1:49,48:97:99:0|1:134948600_C_T:1894,0,2056:134948600 0|1:20,56:76:99:0|1:134948600_C_T:2441,0,656:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:37,44:81:99:0|1:134948600_C_T:1737,0,1630:134948600 0/0:22,0:22:63:.:.:0,63,735:. 0|1:55,94:149:99:0|1:134948600_C_T:3836,0,2074:134948600 0|1:19,27:46:99:0|1:134948600_C_T:1105,0,714:134948600 0|1:30,38:68:99:0|1:134948600_C_T:1617,0,1175:134948600 -chrX 134948635 rs79645126 A C 14726.4 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.035;DB;DP=735;ExcessHet=9.0714;FS=66.587;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=45.42;MQRankSum=-6.252;QD=23.83;ReadPosRankSum=-0.345;SOR=2.865;VQSLOD=-38.84;culprit=MQ;CSQ=C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1443T>G|||||||||-1||HGNC|33269|||||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-480T>G|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,C|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-480T>G|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.434903;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.42377;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=3;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=2;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:32,49:81:99:0|1:134948600_C_T:1928,0,1244:134948600 0/0:19,0:19:51:.:.:0,51,765:. 0|1:48,49:97:99:0|1:134948600_C_T:1897,0,2014:134948600 0|1:19,61:80:99:0|1:134948600_C_T:2441,0,656:134948600 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:36,46:82:99:0|1:134948600_C_T:1774,0,1501:134948600 0/0:22,0:22:63:.:.:0,63,735:. 0|1:58,97:155:99:0|1:134948600_C_T:3861,0,2079:134948600 0|1:19,29:48:99:0|1:134948600_C_T:1135,0,711:134948600 0|1:30,45:75:99:0|1:134948600_C_T:1708,0,1124:134948600 -chrX 134948709 . C T 5029.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=2.11;DP=1113;ExcessHet=9.0714;FS=22.023;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=37.91;MQRankSum=2.79;QD=5.06;ReadPosRankSum=-0.122;SOR=0.396;VQSLOD=-10.5;culprit=MQ;CSQ=T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1369G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-554G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-554G>A|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.293792;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.302233;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:103,15:118:99:0|1:134948709_C_T:306,0,4290:134948709 0/0:26,0:26:78:.:.:0,78,844:. 0|1:101,23:124:99:0|1:134948709_C_T:638,0,4104:134948709 0|1:101,20:121:99:0|1:134948709_C_T:525,0,4142:134948709 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:102,22:124:99:0|1:134948709_C_T:617,0,4203:134948709 0/0:18,0:18:51:.:.:0,51,765:. 0|1:255,60:315:99:0|1:134948709_C_T:1636,0,10052:134948709 0|1:50,19:69:99:0|1:134948709_C_T:623,0,1978:134948709 0|1:98,24:122:99:0|1:134948709_C_T:702,0,3904:134948709 -chrX 134948718 rs371407110 C T 5028.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=0.15;DB;DP=1082;ExcessHet=9.0714;FS=21.995;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=37.69;MQRankSum=2.47;QD=5.23;ReadPosRankSum=0.147;SOR=0.466;VQSLOD=-10.47;culprit=MQ;CSQ=T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1360G>A|||||||||-1||HGNC|33269|||||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-563G>A|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,T|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-563G>A|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.287569;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.296629;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:38,0:38:99:.:.:0,103,1287:. 0|1:105,14:119:99:0|1:134948709_C_T:269,0,4332:134948709 0/0:28,0:28:81:.:.:0,81,933:. 0|1:101,21:122:99:0|1:134948709_C_T:572,0,4176:134948709 0|1:102,20:122:99:0|1:134948709_C_T:506,0,4229:134948709 0/0:37,0:37:99:.:.:0,99,1272:. 0|1:102,23:125:99:0|1:134948709_C_T:646,0,4194:134948709 0/0:18,0:18:54:.:.:0,54,585:. 0|1:229,57:286:99:0|1:134948709_C_T:1662,0,9549:134948709 0|1:48,20:68:99:0|1:134948709_C_T:658,0,1961:134948709 0|1:94,25:119:99:0|1:134948709_C_T:733,0,3850:134948709 -chrX 134948824 rs143758909 G A 2988.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=2.06;DB;DP=752;ExcessHet=9.0714;FS=0.606;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=28.95;MQRankSum=0.666;QD=4.61;ReadPosRankSum=0.497;SOR=0.787;VQSLOD=-9.321;culprit=MQ;CSQ=A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+1254C>T|||||||||-1||HGNC|33269|||||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.170-669C>T|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,A|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.170-669C>T|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.374159;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.36645;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=1;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=1;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,103,1287 0/1:74,23:97:99:428,0,1952 0/0:16,0:16:48:0,48,556 0/1:86,25:111:99:433,0,2206 0/1:66,18:84:99:298,0,1726 0/0:34,0:34:90:0,90,1350 0/1:68,20:88:99:342,0,1719 0/0:16,0:16:48:0,48,536 0/1:98,34:132:99:595,0,2318 0/1:31,17:48:99:353,0,658 0/1:60,28:88:99:557,0,1405 -chrX 134949149 rs138614224 A G 1907.42 VQSRTrancheSNP99.90to100.00 AC=7;AF=0.318;AN=22;BaseQRankSum=-0.514;DB;DP=387;ExcessHet=9.0714;FS=3.677;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=27.22;MQRankSum=-0.372;QD=6.81;ReadPosRankSum=1.72;SOR=0.929;VQSLOD=-10.09;culprit=MQ;CSQ=G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000370724|protein_coding||2/4|ENST00000370724.3:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A4|ENSG00000228836|Transcript|ENST00000420087|protein_coding||2/4|ENST00000420087.2:c.169+929T>C|||||||||-1||HGNC|33269|||||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000463085|protein_coding||2/4|ENST00000463085.2:c.169+929T>C|||||||||-1||HGNC|33270|YES|CCDS35406.1|||,G|intron_variant|MODIFIER|CT45A5|ENSG00000242284|Transcript|ENST00000491480|protein_coding||2/4|ENST00000491480.1:c.169+929T>C|||||||||-1||HGNC|33270||CCDS35406.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.407801;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.401294;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:40,0:40:99:0,117,1371 0/1:29,14:43:99:258,0,699 0/0:20,0:20:60:0,60,645 0/1:41,15:56:99:253,0,999 0/1:17,12:29:99:243,0,408 0/0:25,0:25:72:0,72,859 0/1:33,14:47:99:245,0,824 0/0:22,0:22:63:0,63,759 0/1:30,21:51:99:420,0,664 0/1:12,6:18:90:90,0,274 0/1:16,20:36:99:416,0,320 -chrX 140078339 . T C 2930.69 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=1.05;DP=406;ExcessHet=9.0714;FS=1.994;InbreedingCoeff=-0.4713;MLEAC=7;MLEAF=0.318;MQ=57.31;MQRankSum=0.195;NEGATIVE_TRAIN_SITE;QD=9.9;ReadPosRankSum=0.441;SOR=0.577;VQSLOD=-2.305;culprit=MQ;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-298A8.2|ENSG00000229269|Transcript|ENST00000413328|lincRNA||1/2|ENST00000413328.1:n.124-475T>C|||||||||1||Clone_based_vega_gene||YES||||;cadd_phred=-1;gno_non_neuro_af_all=0.146135;gno_non_neuro_af_nfe=0.141665;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_nfe=0;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:32,0:32:90:0,90,1350 0/1:31,11:42:99:257,0,907 0/0:21,0:21:54:0,54,810 0/1:37,17:54:99:416,0,1121 0/1:14,21:35:99:624,0,371 0/0:41,0:41:99:0,101,1355 0/1:26,13:39:99:335,0,763 0/0:16,0:16:13:0,13,487 0/1:34,17:51:99:427,0,1020 0/1:16,10:26:99:269,0,453 0/1:26,23:49:99:620,0,746 -chrX 140780417 rs113890298 A G 818.27 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.672;DB;DP=307;ExcessHet=9.0714;FS=13.067;InbreedingCoeff=-0.4558;MLEAC=7;MLEAF=0.318;MQ=55.06;MQRankSum=-2.028;NEGATIVE_TRAIN_SITE;QD=4.2;ReadPosRankSum=1.22;SOR=0.179;VQSLOD=-2.505;culprit=MQ;CSQ=G|intergenic_variant|MODIFIER|||||||||||||||||||||||||;cadd_phred=-1;gno_non_neuro_af_all=0.0578861;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0275727;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=0;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;highest_impact_order=64;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:36,0:36:99:.:.:0,99,1485:. 0/1:31,4:35:74:.:.:74,0,1325:. 0/0:26,0:26:69:.:.:0,69,1035:. 0/1:33,3:36:9:.:.:9,0,1424:. 0/1:14,4:18:99:.:.:126,0,489:. 0/0:36,0:36:99:.:.:0,99,1271:. 0|1:19,4:23:99:0|1:140780392_G_A:111,0,792:140780392 0/0:14,0:14:42:.:.:0,42,426:. 0/1:31,3:34:33:.:.:33,0,1156:. 0/1:13,7:20:99:.:.:255,0,497:. 0/1:22,7:29:99:.:.:228,0,810:. -chrX 140785739 rs149295712 A C 1949.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-0.057;DB;DP=424;ExcessHet=9.0714;FS=1.077;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=57.28;MQRankSum=-3.626;NEGATIVE_TRAIN_SITE;QD=6.21;ReadPosRankSum=-0.446;SOR=0.805;VQSLOD=-2.108;culprit=MQ;CSQ=C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.177T>G|ENSP00000359546.3:p.Phe59Leu|511/682|177/294|59/97|F/L|ttT/ttG|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.3)|benign(0.003)|;cadd_phred=-1;gno_non_neuro_af_all=0.0596689;gno_non_neuro_af_nfe=0.0522111;gno_non_neuro_nhomalt_all=4;gno_non_neuro_nhomalt_nfe=0;impactful;genic;highest_impact_order=14;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:36,0:36:99:.:.:0,101,1287:. 0|1:25,13:38:99:0|1:140785739_A_C:467,0,1032:140785739 0/0:16,0:16:34:.:.:0,34,507:. 0|1:37,10:47:99:0|1:140785739_A_C:306,0,1543:140785739 0|1:17,17:34:99:0|1:140785739_A_C:663,0,981:140785739 0/0:38,0:38:99:.:.:0,105,1285:. 0|1:45,5:50:71:0|1:140785739_A_C:71,0,1906:140785739 0/0:20,0:20:60:.:.:0,60,675:. 0|1:64,8:72:99:0|1:140785739_A_C:140,0,4030:140785739 0|1:28,6:34:99:0|1:140785739_A_C:167,0,1483:140785739 0|1:33,6:39:99:0|1:140785739_A_C:153,0,1884:140785739 -chrX 140785741 rs144554749 A C 1949.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=-1.394;DB;DP=422;ExcessHet=9.0714;FS=1.692;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=57.32;MQRankSum=-3.694;NEGATIVE_TRAIN_SITE;QD=6.25;ReadPosRankSum=-0.164;SOR=0.822;VQSLOD=-2.102;culprit=MQRankSum;CSQ=C|missense_variant|MODERATE|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding|2/2||ENST00000370515.3:c.175T>G|ENSP00000359546.3:p.Phe59Val|509/682|175/294|59/97|F/V|Ttt/Gtt|||-1||HGNC|14332|YES|CCDS14675.1|tolerated_low_confidence(0.74)|benign(0)|;cadd_phred=-1;gno_non_neuro_af_all=0.103136;gno_non_neuro_af_all_filter;gno_non_neuro_af_nfe=0.0958019;gno_non_neuro_af_nfe_filter;gno_non_neuro_nhomalt_all=4;gno_non_neuro_nhomalt_all_filter;gno_non_neuro_nhomalt_nfe=0;gno_non_neuro_nhomalt_nfe_filter;impactful;genic;highest_impact_order=14;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:36,0:36:99:.:.:0,101,1287:. 0|1:26,13:39:99:0|1:140785739_A_C:467,0,1032:140785739 0/0:16,0:16:45:.:.:0,45,675:. 0|1:38,10:48:99:0|1:140785739_A_C:306,0,1543:140785739 0|1:17,17:34:99:0|1:140785739_A_C:663,0,981:140785739 0/0:38,0:38:99:.:.:0,105,1285:. 0|1:46,5:51:71:0|1:140785739_A_C:71,0,1906:140785739 0/0:20,0:20:60:.:.:0,60,675:. 0|1:61,8:69:99:0|1:140785739_A_C:140,0,4030:140785739 0|1:27,6:33:99:0|1:140785739_A_C:167,0,1483:140785739 0|1:32,6:38:99:0|1:140785739_A_C:153,0,1884:140785739 -chrX 140785855 rs146412887 A G 2911.42 PASS AC=7;AF=0.318;AN=22;BaseQRankSum=0.845;DB;DP=435;ExcessHet=9.0714;FS=2.507;InbreedingCoeff=-0.4667;MLEAC=7;MLEAF=0.318;MQ=57.08;MQRankSum=-0.85;NEGATIVE_TRAIN_SITE;QD=8.93;ReadPosRankSum=0.412;SOR=0.555;VQSLOD=-2.355;culprit=MQ;CSQ=G|intron_variant|MODIFIER|SPANXD|ENSG00000196406|Transcript|ENST00000370515|protein_coding||1/1|ENST00000370515.3:c.73-12T>C|||||||||-1||HGNC|14332|YES|CCDS14675.1|||;cadd_phred=-1;gno_non_neuro_af_all=0.155131;gno_non_neuro_af_nfe=0.149268;gno_non_neuro_nhomalt_all=2;gno_non_neuro_nhomalt_nfe=1;highest_impact_order=47;aff_only=C0011JZ,C0011K2,C0011K3,C0011KA,IP00FNP,IP00FNW,IP00FNY GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,103,1287 0/1:28,17:45:99:421,0,762 0/0:20,0:20:60:0,60,675 0/1:28,12:40:99:294,0,820 0/1:19,22:41:99:641,0,517 0/0:31,0:31:90:0,90,1058 0/1:35,11:46:99:244,0,1052 0/0:20,0:20:57:0,57,855 0/1:40,13:53:99:288,0,1191 0/1:32,18:50:99:465,0,936 0/1:30,21:51:99:576,0,870 diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/Log_info.txt b/example of results/PL_family_WGS_slivar_1664807682/reports/Log_info.txt similarity index 100% rename from example of results/PL_family_WGS_slivar_1664357562/reports/Log_info.txt rename to example of results/PL_family_WGS_slivar_1664807682/reports/Log_info.txt diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/Run_info.txt b/example of results/PL_family_WGS_slivar_1664807682/reports/Run_info.txt similarity index 88% rename from example of results/PL_family_WGS_slivar_1664357562/reports/Run_info.txt rename to example of results/PL_family_WGS_slivar_1664807682/reports/Run_info.txt index 031f0be..561f62a 100644 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/Run_info.txt +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/Run_info.txt @@ -1,9 +1,9 @@ Project (empty means no .git folder where the main.nf file is present): origin git@gitlab.pasteur.fr:gmillot/slivar_vcf_extraction.git (fetch) -Git info (empty means no .git folder where the main.nf file is present): v1.3-5-g452bdf066b-dirty +Git info (empty means no .git folder where the main.nf file is present): v1.0-1-g39d9669a0a-dirty Cmd line: nextflow run slivar_vcf_extraction.nf -c slivar_vcf_extraction.config execution mode: local Manifest's pipeline version: null -result path: /mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/results/PL_family_WGS_slivar_1664357562 +result path: /mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/results/PL_family_WGS_slivar_1664807682 nextflow version: 21.04.2 @@ -16,5 +16,5 @@ workDir (directory where tasks temporary files are created): /mnt/c/Users/Gael/D USER VARIABLES: -out_path: /mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/results/PL_family_WGS_slivar_1664357562 +out_path: /mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/results/PL_family_WGS_slivar_1664807682 sample_path: /mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf diff --git a/example of results/PL_family_WGS_slivar_1664807682/reports/dag.dot b/example of results/PL_family_WGS_slivar_1664807682/reports/dag.dot new file mode 100644 index 0000000..3902689 --- /dev/null +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/dag.dot @@ -0,0 +1,70 @@ +digraph "dag" { +p1 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p1 -> p9 [label="vcf"]; + +p2 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p2 -> p9 [label="fun"]; + +p3 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p3 -> p9 [label="annot1"]; + +p4 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p4 -> p9 [label="annot2"]; + +p5 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p5 -> p9 [label="ped"]; + +p6 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p6 -> p9 [label="sample_expr"]; + +p7 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p7 -> p9 [label="pedigree_expr"]; + +p8 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p8 -> p9 [label="filter"]; + +p9 [label="slivar_extract"]; +p14 [label="slivar_tsv"]; +p9 -> p14 [label="vcf_ch1"]; + +p9 [label="slivar_extract"]; +p15 [label="slivar_vcf_compress"]; +p9 -> p15 [label="vcf_ch2"]; + +p10 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p10 -> p14 [label="ped"]; + +p11 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p11 -> p14 [label="tsv_file"]; + +p12 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p12 -> p14 [label="tsv_sample"]; + +p13 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p13 -> p14 [label="tsv_info"]; + +p16 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p16 -> p19 [label="config_file"]; + +p17 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p17 -> p19 [label="log_file"]; + +p18 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p18 -> p19 [label="fun"]; + +} diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/report.html b/example of results/PL_family_WGS_slivar_1664807682/reports/report.html similarity index 99% rename from example of results/PL_family_WGS_slivar_1664357562/reports/report.html rename to example of results/PL_family_WGS_slivar_1664807682/reports/report.html index 13f79b6..f1d8fb7 100644 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/report.html +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/report.html @@ -18,11 +18,11 @@ <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> - <meta name="description" content="Nextflow workflow report for run id [suspicious_yalow]"> + <meta name="description" content="Nextflow workflow report for run id [focused_volta]"> <meta name="author" content="Paolo Di Tommaso, Phil Ewels"> <link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" /> - <title>[suspicious_yalow] Nextflow Workflow Report</title> + <title>[focused_volta] Nextflow Workflow Report</title> <style type="text/css"> /*! @@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li> </ul> <span class="navbar-text"> - [suspicious_yalow] + [focused_volta] </span> </div> </nav> @@ -146,7 +146,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <div class="container"> <h1 class="display-3">Nextflow workflow report</h1> - <h2 class="text-muted mb-4"><samp>[suspicious_yalow]</samp> </h2> + <h2 class="text-muted mb-4"><samp>[focused_volta]</samp> </h2> <div class="alert alert-success mb-4"> @@ -157,13 +157,13 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <dl> <dt>Run times</dt> <dd> - <span id="workflow_start">28-Sep-2022 11:32:42</span> - <span id="workflow_complete">28-Sep-2022 11:32:53</span> - (<span id="completed_fromnow"></span>duration: <strong>10.8s</strong>) + <span id="workflow_start">03-Oct-2022 16:34:43</span> - <span id="workflow_complete">03-Oct-2022 16:34:55</span> + (<span id="completed_fromnow"></span>duration: <strong>12.6s</strong>) </dd> <dl> <div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;"> - <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="3 tasks succeeded"><span class="text-truncate"> 3 succeeded </span></div> + <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="5 tasks succeeded"><span class="text-truncate"> 5 succeeded </span></div> <div style="width: 0.0%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="0 tasks were cached"><span class="text-truncate"> 0 cached </span></div> <div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate"> 0 ignored </span></div> <div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate"> 0 failed </span></div> @@ -194,11 +194,11 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <dt class="col-sm-3">Script ID</dt> - <dd class="col-sm-9"><code>b387dfea1094fd5899f166cfbb37f1e0</code></dd> + <dd class="col-sm-9"><code>b87d6c38210d9b4a1d499d15b1c6cbd4</code></dd> <dt class="col-sm-3">Workflow session</dt> - <dd class="col-sm-9"><code>ea497845-b633-4ffc-b380-3c83bc468222</code></dd> + <dd class="col-sm-9"><code>06a96f6a-23c3-4218-a070-438fd6c89dad</code></dd> @@ -1029,7 +1029,7 @@ $(function() { // Nextflow report data window.data = { "trace":[ -{"task_id":"3","hash":"43\/9f2a52","native_id":"4517","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/Gael\/Documents\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1664357563464","start":"1664357563551","complete":"1664357564319","duration":"855","realtime":"8","%cpu":"10.1","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"106576","wchar":"339","syscr":"189","syscw":"14","read_bytes":"329728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\/43\/9f2a52036364e9e6d791086c88465c","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:sample.DP >= 0\'\npedigree_expr= \nfilter=false\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664357562\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= 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","scratch":"-","queue":"-","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:sample.DP >= 0\'\npedigree_expr= \nfilter=false\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i 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\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run slivar_vcf_extraction.nf -c slivar_vcf_extraction.config\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664357562\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664357562\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:sample.DP >= 0\'\npedigree_expr= \nfilter=false\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i 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}; +{"task_id":"2","hash":"01\/27568e","native_id":"30957","process":"slivar_extract","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_extract","status":"COMPLETED","exit":"0","submit":"1664807684296","start":"1664807684394","complete":"1664807694321","duration":"10025","realtime":"9270","%cpu":"51.5","%mem":"1.9","rss":"2010443776","vmem":"2027454464","peak_rss":"2010443776","peak_vmem":"2027470848","rchar":"459619277","wchar":"48902","syscr":"50216","syscw":"51","read_bytes":"4819968","write_bytes":"24576","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\/01\/27568e269289082b0e2124e466a8c7","script":"\n #!\/bin\/bash -ue\n slivar expr --js slivar-functions.js -g cadd-1.6-SNVs-phred10-GRCh37.zip -g gnomad-2.1.1-genome-GRCh37.zip --vcf Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf --ped Dyslexia.pedigree.txt --sample-expr \'all:true\' -o \"res.vcf\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:true\'\npedigree_expr= \nfilter=false\ntsv_file=true\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= 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Log_info.txt\n ","scratch":"-","queue":"-","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:true\'\npedigree_expr= \nfilter=false\ntsv_file=true\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"1","hash":"89\/bbad7c","native_id":"31038","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1664807684392","start":"1664807684476","complete":"1664807685591","duration":"1199","realtime":"383","%cpu":"18.8","%mem":"0.0","rss":"3293184","vmem":"20156416","peak_rss":"3293184","peak_vmem":"20156416","rchar":"137032","wchar":"1615","syscr":"266","syscw":"35","read_bytes":"3517440","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\/89\/bbad7cc1955cae43ec30d3b362fabb","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run slivar_vcf_extraction.nf -c slivar_vcf_extraction.config\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:true\'\npedigree_expr= \nfilter=false\ntsv_file=true\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin:$PATH\n","error_action":"-","vol_ctxt":"11","inv_ctxt":"0"},{"task_id":"5","hash":"48\/02cb61","native_id":"31888","process":"slivar_vcf_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_vcf_compress","status":"COMPLETED","exit":"0","submit":"1664807694372","start":"1664807694421","complete":"1664807694951","duration":"579","realtime":"70","%cpu":"30.1","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"221825","wchar":"10489","syscr":"294","syscw":"15","read_bytes":"1383424","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\/48\/02cb61a13d995e40326166b35d5dc1","script":"\n #!\/bin\/bash -ue\n bgzip -cf -l 9 res.vcf > res.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n tabix -p vcf res.vcf.gz # htslib command\n ","scratch":"-","queue":"-","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:true\'\npedigree_expr= \nfilter=false\ntsv_file=true\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"4","hash":"6d\/2633c5","native_id":"32040","process":"slivar_tsv","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_tsv","status":"COMPLETED","exit":"0","submit":"1664807694962","start":"1664807695051","complete":"1664807695722","duration":"760","realtime":"283","%cpu":"20.8","%mem":"0.0","rss":"5492736","vmem":"13643776","peak_rss":"5492736","peak_vmem":"13660160","rchar":"362586","wchar":"166427","syscr":"364","syscw":"120","read_bytes":"4771840","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/work\/6d\/2633c53a2e81e9329af1b85e596a15","script":"\n #!\/bin\/bash -ue\n if [[ true == true ]] ; then \n slivar tsv --ped Dyslexia.pedigree.txt -s all -i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all res.vcf > res.tsv\n gzip -f res.tsv \n fi\n ","scratch":"-","queue":"-","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf\nfun_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin\/slivar-functions.js\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr=--sample-expr \'all:true\'\npedigree_expr= \nfilter=false\ntsv_file=true\ntsv_sample=all\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/results\/PL_family_WGS_slivar_1664807682\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/slivar_vcf_extraction\/bin:$PATH\n","error_action":"-","vol_ctxt":"196","inv_ctxt":"0"}], 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}; </script> diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/slivar-functions.js b/example of results/PL_family_WGS_slivar_1664807682/reports/slivar-functions.js similarity index 100% rename from example of results/PL_family_WGS_slivar_1664357562/reports/slivar-functions.js rename to example of results/PL_family_WGS_slivar_1664807682/reports/slivar-functions.js diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/slivar_vcf_extraction.config b/example of results/PL_family_WGS_slivar_1664807682/reports/slivar_vcf_extraction.config similarity index 90% rename from example of results/PL_family_WGS_slivar_1664357562/reports/slivar_vcf_extraction.config rename to example of results/PL_family_WGS_slivar_1664807682/reports/slivar_vcf_extraction.config index 533248d..1888300 100644 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/slivar_vcf_extraction.config +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/slivar_vcf_extraction.config @@ -27,11 +27,12 @@ env { annot1_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/cadd-1.6-SNVs-phred10-GRCh37.zip" // path of the cadd annotation file. Example : annot1_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/cadd-1.6-SNVs-phred10-GRCh37.zip", annot1_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/references/GRCh37/slivar-gnotate/cadd-1.6-SNVs-phred10-GRCh37.zip" // cadd annotation annot2_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/gnomad-2.1.1-genome-GRCh37.zip" // path of gnomad annotation file. Example : annot2_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/gnomad-2.1.1-genome-GRCh37.zip", annot2_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/references/GRCh37/slivar-gnotate/gnomad-2.1.1-genome-GRCh37.zip" // gnomad annotation - sample_expr = "--sample-expr 'all:sample.DP >= 0'" // expression to use for the --sample-expr option of slivar. Example: sample_expr = "--sample-expr 'high_quality:sample.GQ >= 10'". Before the colon is the name of the new field added in the INFO field of the VCF. Write " " if no selection wanted (only annotation). "--sample-expr 'all:sample.DP >= 0'" Must be used if no filter wanted but tsv wanted. Another example: "--sample-expr 'all:sample.GQ == \".\"'" + sample_expr = "--sample-expr 'all:true'" // expression to use for the --sample-expr option of slivar. Example: sample_expr = "--sample-expr 'high_quality:sample.GQ >= 10'". Before the colon is the name of the new field added in the INFO field of the VCF. Write " " if no selection wanted (only annotation). Write "--sample-expr 'all:true'" if no filter wanted but tsv wanted. Warning: all:sample.DP >= 0 is not equivalent to all:true. Of note, "--sample-expr 'all:sample.GQ == \".\"'" is correctly written in the .command.sh file in the work dir of nextflow, but does not seem to work in selecting the empty GQ pedigree_expr = " " // expression to use for the --family-expr or --trio or --group-expr option of slivar in order to filter the data according to pedigree info or VCF info (depends on the .js file defined by fun_path above). See https://github.com/brentp/slivar#commands for details. Example: "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'". Write " " if no selection wanted (only annotation). Of note, for no filtering, pedigree_expr="all:fam.every(function(s){return s.affected || s.unaffected})" does not work, we have to use --sample-expr filter = "false" // if false, the output VCF is only labeled in the VCF INFO field according to the pedigree_expr parameter. If true, take only the labeled lines (variants) of the output VCF. Of note, true add the --pass-only argument to the slivar expr - tsv_sample = "all" // mandatory -s option of the slivar tsv command. Example sample="aff_only". What is indicated must be a field of the INFO field of the vcf, added using the sample_expr or pedigree_expr parameter - tsv_info = "-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all" // -i option of the slivar tsv command that extracts data from the INFO field of the vcf file (https://github.com/brentp/slivar#tsv) for the tsv file output. Example : "-i AC -i AF -i AN". Warning: if one of the -i is not in the vcf file, it will generate an error. Thus, be carefull with what is used in the sample_expr or pedigree_expr parameter + tsv_file = "true" // if true, return a .tsv file of the .vcf file output + tsv_sample = "all" // mandatory -s option of the slivar tsv command. Example sample="aff_only". What is indicated must be a field of the INFO field of the vcf, added using the sample_expr or pedigree_expr parameter. Ignored if tsv_file == "true" + tsv_info = "-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all" // -i option of the slivar tsv command that extracts data from the INFO field of the vcf file (https://github.com/brentp/slivar#tsv) for the tsv file output. Example : "-i AC -i AF -i AN". Warning: if one of the -i is not in the vcf file, it will generate an error. Thus, be carefull with what is used in the sample_expr or pedigree_expr parameter. Ignored if tsv_file == "true" } //////// end variables that will be used only in the main.nf @@ -137,7 +138,7 @@ singularity { }else if(system_exec == 'slurm_local'){ cacheDir = 'singularity' // "$baseDir/singularity" can be used but do not forget double quotes. }else{ - cacheDir = '/mnt/c/Users/Gael/Documents/singularity' // "$baseDir/singularity" can be used but do not forget double quotes. + cacheDir = '/mnt/c/Users/gmillot/singularity' // "$baseDir/singularity" can be used but do not forget double quotes. } } @@ -169,7 +170,7 @@ process { } withLabel: slivar { - container='gmillot/slivar_v1.0:gitlab_v8.11' + container='gmillot/slivar_v2.0:gitlab_v9.1' cpus=1 memory='60G' } diff --git a/example of results/PL_family_WGS_slivar_1664357562/reports/timeline.html b/example of results/PL_family_WGS_slivar_1664807682/reports/timeline.html similarity index 99% rename from example of results/PL_family_WGS_slivar_1664357562/reports/timeline.html rename to example of results/PL_family_WGS_slivar_1664807682/reports/timeline.html index d1d31f3..ef7bc16 100644 --- a/example of results/PL_family_WGS_slivar_1664357562/reports/timeline.html +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/timeline.html @@ -205,13 +205,15 @@ $(function() { // Nextflow report data window.data = { - "elapsed": "11.2s", - "beginningMillis": 1664357562635, - "endingMillis": 1664357573819, + "elapsed": "13s", + "beginningMillis": 1664807683271, + "endingMillis": 1664807696244, "processes": [ - {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1664357563464, "ending_time": 1664357563551}, {"starting_time": 1664357563551, "ending_time": 1664357563559, "label": "855ms \/ 0"}, {"starting_time": 1664357563559, "ending_time": 1664357564319}]}, - {"label": "slivar", "cached": false, "index": 1, "times": [{"starting_time": 1664357563516, "ending_time": 1664357563586}, {"starting_time": 1664357563586, "ending_time": 1664357572769, "label": "9.8s \/ 1.9 GB"}, {"starting_time": 1664357572769, "ending_time": 1664357573302}]}, - {"label": "WorkflowVersion", "cached": false, "index": 2, "times": [{"starting_time": 1664357563565, "ending_time": 1664357563650}, {"starting_time": 1664357563650, "ending_time": 1664357564119, "label": "1.2s \/ 3.1 MB"}, {"starting_time": 1664357564119, "ending_time": 1664357564802}]} + {"label": "slivar_extract", "cached": false, "index": 0, "times": [{"starting_time": 1664807684296, "ending_time": 1664807684394}, {"starting_time": 1664807684394, "ending_time": 1664807693664, "label": "10s \/ 1.9 GB"}, {"starting_time": 1664807693664, "ending_time": 1664807694321}]}, + {"label": "Backup", "cached": false, "index": 1, "times": [{"starting_time": 1664807684347, "ending_time": 1664807684431}, {"starting_time": 1664807684431, "ending_time": 1664807684437, "label": "836ms \/ 0"}, {"starting_time": 1664807684437, "ending_time": 1664807685183}]}, + {"label": "WorkflowVersion", "cached": false, "index": 2, "times": [{"starting_time": 1664807684392, "ending_time": 1664807684476}, {"starting_time": 1664807684476, "ending_time": 1664807684859, "label": "1.2s \/ 3.1 MB"}, {"starting_time": 1664807684859, "ending_time": 1664807685591}]}, + {"label": "slivar_vcf_compress", "cached": false, "index": 3, "times": [{"starting_time": 1664807694372, "ending_time": 1664807694421}, {"starting_time": 1664807694421, "ending_time": 1664807694491, "label": "579ms \/ 0"}, {"starting_time": 1664807694491, "ending_time": 1664807694951}]}, + {"label": "slivar_tsv", "cached": false, "index": 4, "times": [{"starting_time": 1664807694962, "ending_time": 1664807695051}, {"starting_time": 1664807695051, "ending_time": 1664807695334, "label": "760ms \/ 5.2 MB"}, {"starting_time": 1664807695334, "ending_time": 1664807695722}]} ] } ; diff --git a/example of results/PL_family_WGS_slivar_1664807682/reports/trace.txt b/example of results/PL_family_WGS_slivar_1664807682/reports/trace.txt new file mode 100644 index 0000000..c1614aa --- /dev/null +++ b/example of results/PL_family_WGS_slivar_1664807682/reports/trace.txt @@ -0,0 +1,6 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar +3 2c/6005d5 30992 Backup COMPLETED 0 2022-10-03 16:34:44.347 836ms 6ms 20.5% 0 0 104.2 KB 345 B +1 89/bbad7c 31038 WorkflowVersion COMPLETED 0 2022-10-03 16:34:44.392 1.2s 383ms 18.8% 3.1 MB 19.2 MB 133.8 KB 1.6 KB +2 01/27568e 30957 slivar_extract COMPLETED 0 2022-10-03 16:34:44.296 10s 9.3s 51.5% 1.9 GB 1.9 GB 438.3 MB 47.8 KB +5 48/02cb61 31888 slivar_vcf_compress COMPLETED 0 2022-10-03 16:34:54.372 579ms 70ms 30.1% 0 0 216.6 KB 10.2 KB +4 6d/2633c5 32040 slivar_tsv COMPLETED 0 2022-10-03 16:34:54.962 760ms 283ms 20.8% 5.2 MB 13 MB 354.1 KB 162.5 KB diff --git a/example of results/PL_family_WGS_slivar_1664807682/res.tsv.gz b/example of results/PL_family_WGS_slivar_1664807682/res.tsv.gz new file mode 100644 index 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results/PL_family_WGS_slivar_1664813804/reports/Run_info.txt @@ -1,10 +1,10 @@ Project (empty means no .git folder where the main.nf file is present): Git info (empty means no .git folder where the main.nf file is present): -Cmd line: nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git slivar_vcf_extraction_v1.6.nf -c slivar_vcf_extraction.config +Cmd line: nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git slivar_vcf_extraction_v2.0.nf -c slivar_vcf_extraction.config -resume execution mode: slurm loaded modules (according to specification by the user thanks to the --modules argument of main.nf): /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git Manifest's pipeline version: null -result path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_slivar_1664358140 +result path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_slivar_1664813804 nextflow version: 21.04.1 @@ -17,5 +17,5 @@ workDir (directory where tasks temporary files are created): /pasteur/zeus/proje USER VARIABLES: -out_path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_slivar_1664358140 +out_path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_slivar_1664813804 sample_path: /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz diff --git a/example of results/PL_family_WGS_slivar_1664813804/reports/dag.dot b/example of results/PL_family_WGS_slivar_1664813804/reports/dag.dot new file mode 100644 index 0000000..3902689 --- /dev/null +++ b/example of results/PL_family_WGS_slivar_1664813804/reports/dag.dot @@ -0,0 +1,70 @@ +digraph "dag" { +p1 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p1 -> p9 [label="vcf"]; + +p2 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p2 -> p9 [label="fun"]; + +p3 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p3 -> p9 [label="annot1"]; + +p4 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p4 -> p9 [label="annot2"]; + +p5 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p5 -> p9 [label="ped"]; + +p6 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p6 -> p9 [label="sample_expr"]; + +p7 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p7 -> p9 [label="pedigree_expr"]; + +p8 [shape=point,label="",fixedsize=true,width=0.1]; +p9 [label="slivar_extract"]; +p8 -> p9 [label="filter"]; + +p9 [label="slivar_extract"]; +p14 [label="slivar_tsv"]; +p9 -> p14 [label="vcf_ch1"]; + +p9 [label="slivar_extract"]; +p15 [label="slivar_vcf_compress"]; +p9 -> p15 [label="vcf_ch2"]; + +p10 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p10 -> p14 [label="ped"]; + +p11 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p11 -> p14 [label="tsv_file"]; + +p12 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p12 -> p14 [label="tsv_sample"]; + +p13 [shape=point,label="",fixedsize=true,width=0.1]; +p14 [label="slivar_tsv"]; +p13 -> p14 [label="tsv_info"]; + +p16 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p16 -> p19 [label="config_file"]; + +p17 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p17 -> p19 [label="log_file"]; + +p18 [shape=point,label="",fixedsize=true,width=0.1]; +p19 [label="Backup"]; +p18 -> p19 [label="fun"]; + +} diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/report.html b/example of results/PL_family_WGS_slivar_1664813804/reports/report.html similarity index 99% rename from example of results/PL_family_WGS_slivar_1664358140/reports/report.html rename to example of results/PL_family_WGS_slivar_1664813804/reports/report.html index 116a9cf..fec64ea 100644 --- a/example of results/PL_family_WGS_slivar_1664358140/reports/report.html +++ b/example of results/PL_family_WGS_slivar_1664813804/reports/report.html @@ -18,11 +18,11 @@ <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> - <meta name="description" content="Nextflow workflow report for run id [goofy_kimura]"> + <meta name="description" content="Nextflow workflow report for run id [festering_feynman]"> <meta name="author" content="Paolo Di Tommaso, Phil Ewels"> <link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" /> - <title>[goofy_kimura] Nextflow Workflow Report</title> + <title>[festering_feynman] Nextflow Workflow Report</title> <style type="text/css"> /*! @@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li> </ul> <span class="navbar-text"> - [goofy_kimura] + [festering_feynman] </span> </div> </nav> @@ -146,7 +146,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <div class="container"> <h1 class="display-3">Nextflow workflow report</h1> - <h2 class="text-muted mb-4"><samp>[goofy_kimura]</samp> </h2> + <h2 class="text-muted mb-4"><samp>[festering_feynman]</samp> <em>(resumed run)</em></h2> <div class="alert alert-success mb-4"> @@ -157,13 +157,13 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <dl> <dt>Run times</dt> <dd> - <span id="workflow_start">28-Sep-2022 11:42:20</span> - <span id="workflow_complete">28-Sep-2022 12:00:01</span> - (<span id="completed_fromnow"></span>duration: <strong>17m 41s</strong>) + <span id="workflow_start">03-Oct-2022 18:16:44</span> - <span id="workflow_complete">03-Oct-2022 18:36:55</span> + (<span id="completed_fromnow"></span>duration: <strong>20m 11s</strong>) </dd> <dl> <div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;"> - <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="3 tasks succeeded"><span class="text-truncate"> 3 succeeded </span></div> + <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="5 tasks succeeded"><span class="text-truncate"> 5 succeeded </span></div> <div style="width: 0.0%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="0 tasks were cached"><span class="text-truncate"> 0 cached </span></div> <div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate"> 0 ignored </span></div> <div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate"> 0 failed </span></div> @@ -171,7 +171,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r </dl> <dt>Nextflow command</dt> - <dd><pre class="nfcommand"><code>nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git slivar_vcf_extraction_v1.6.nf -c slivar_vcf_extraction.config</code></pre></dd> + <dd><pre class="nfcommand"><code>nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git slivar_vcf_extraction_v2.0.nf -c slivar_vcf_extraction.config -resume</code></pre></dd> </dl> <dl class="row small"> @@ -189,16 +189,16 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r <dt class="col-sm-3">Script name</dt> - <dd class="col-sm-9"><samp>slivar_vcf_extraction_v1.6.nf</samp></dd> + <dd class="col-sm-9"><samp>slivar_vcf_extraction_v2.0.nf</samp></dd> <dt class="col-sm-3">Script ID</dt> - <dd class="col-sm-9"><code>b387dfea1094fd5899f166cfbb37f1e0</code></dd> + <dd class="col-sm-9"><code>b87d6c38210d9b4a1d499d15b1c6cbd4</code></dd> <dt class="col-sm-3">Workflow session</dt> - <dd class="col-sm-9"><code>5cfc7283-1e20-441a-854c-0680c72eb8ad</code></dd> + <dd class="col-sm-9"><code>898fb66a-5d40-4ab5-af9e-0d737a5a9c93</code></dd> @@ -1029,7 +1029,7 @@ $(function() { // Nextflow report data window.data = { "trace":[ -{"task_id":"3","hash":"00\/e6eb69","native_id":"29539507","process":"Backup","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1664358141685","start":"1664358146339","complete":"1664358151345","duration":"9660","realtime":"14","%cpu":"5.4","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"125212","wchar":"1529","syscr":"189","syscw":"32","read_bytes":"246784","write_bytes":"4096","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/00\/e6eb69f1c1595da38f89788ebfb60e","script":"\n echo -e \"full .nextflow.log is in: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664358140\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"1","hash":"60\/eb369a","native_id":"29539508","process":"WorkflowVersion","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1664358141744","start":"1664358146432","complete":"1664358151396","duration":"9652","realtime":"519","%cpu":"4.6","%mem":"0.0","rss":"5459968","vmem":"40321024","peak_rss":"5459968","peak_vmem":"40321024","rchar":"154756","wchar":"3365","syscr":"234","syscw":"59","read_bytes":"1081344","write_bytes":"40960","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/60\/eb369a2658a923951639e25a8f52b4","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run --modules \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git slivar_vcf_extraction_v1.6.nf -c slivar_vcf_extraction.config\" >> Run_info.txt\n echo \"execution mode\": slurm >> Run_info.txt\n modules=\/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664358140\" >> Run_info.txt\n echo \"nextflow version: 21.04.1\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nprojectDir (directory where the main.nf script is located): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nworkDir (directory where tasks temporary files are created): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664358140\\nsample_path: \/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664358140\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"5","inv_ctxt":"2"},{"task_id":"2","hash":"36\/8a923b","native_id":"29539509","process":"slivar","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-slivar_v1.0-gitlab_v8.11.img","tag":"-","name":"slivar","status":"COMPLETED","exit":"0","submit":"1664358141799","start":"1664358151410","complete":"1664359201394","duration":"1059595","realtime":"1050761","%cpu":"95.3","%mem":"0.4","rss":"2402795520","vmem":"2421927936","peak_rss":"2402795520","peak_vmem":"2421940224","rchar":"6975109311","wchar":"868474","syscr":"633172","syscw":"578","read_bytes":"6379201536","write_bytes":"892928","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/36\/8a923b77dcdac854fce42f41d71da7","script":"\n #!\/bin\/bash -ue\n\n # add the modification of the pedigree if \n slivar expr --js slivar-functions.js -g cadd-1.6-SNVs-phred10-GRCh37.zip -g gnomad-2.1.1-genome-GRCh37.zip --vcf Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz --ped Dyslexia.pedigree.txt --family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\' --pass-only -o \"res.vcf\"\n slivar tsv --ped Dyslexia.pedigree.txt -s aff_only -i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only res.vcf > res.tsv\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664358140\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"2560","inv_ctxt":"315069"}], 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}; +{"task_id":"3","hash":"38\/934009","native_id":"30751438","process":"Backup","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1664813805968","start":"1664813810695","complete":"1664813810712","duration":"4744","realtime":"54","%cpu":"7.2","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"125029","wchar":"1528","syscr":"189","syscw":"32","read_bytes":"246784","write_bytes":"4096","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/38\/934009545f70cc1f02a3a3c2bde210","script":"\n echo -e \"full .nextflow.log is in: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_file=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"1","hash":"fc\/31bb4d","native_id":"30751439","process":"WorkflowVersion","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1664813806018","start":"1664813810762","complete":"1664813810780","duration":"4762","realtime":"141","%cpu":"20.9","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"154598","wchar":"3373","syscr":"234","syscw":"59","read_bytes":"1081344","write_bytes":"40960","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/fc\/31bb4d59280a16c4457782eaee46ad","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run --modules \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git slivar_vcf_extraction_v2.0.nf -c slivar_vcf_extraction.config -resume\" >> Run_info.txt\n echo \"execution mode\": slurm >> Run_info.txt\n modules=\/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\" >> Run_info.txt\n echo \"nextflow version: 21.04.1\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nprojectDir (directory where the main.nf script is located): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nworkDir (directory where tasks temporary files are created): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\\nsample_path: \/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"3221225472","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_file=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"2","hash":"aa\/876012","native_id":"30751640","process":"slivar_extract","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_extract","status":"COMPLETED","exit":"0","submit":"1664813990423","start":"1664813995703","complete":"1664815010753","duration":"1020330","realtime":"1016118","%cpu":"97.8","%mem":"0.4","rss":"2398576640","vmem":"2424942592","peak_rss":"2398576640","peak_vmem":"2424958976","rchar":"6974975542","wchar":"214833","syscr":"633229","syscw":"106","read_bytes":"2161664","write_bytes":"237568","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/aa\/876012a3be8c8c258a7cea70862e19","script":"\n #!\/bin\/bash -ue\n slivar expr --js slivar-functions.js -g cadd-1.6-SNVs-phred10-GRCh37.zip -g gnomad-2.1.1-genome-GRCh37.zip --vcf Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz --ped Dyslexia.pedigree.txt --family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\' --pass-only -o \"res.vcf\"\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_file=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"190","inv_ctxt":"313710"},{"task_id":"5","hash":"73\/a5ca3a","native_id":"30753324","process":"slivar_vcf_compress","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_vcf_compress","status":"COMPLETED","exit":"0","submit":"1664815010820","start":"1664815015752","complete":"1664815015770","duration":"4950","realtime":"138","%cpu":"25.8","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"436774","wchar":"48068","syscr":"296","syscw":"32","read_bytes":"1001472","write_bytes":"49152","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/73\/a5ca3af86ed4f8f19d74b3af111d55","script":"\n #!\/bin\/bash -ue\n bgzip -cf -l 9 res.vcf > res.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n tabix -p vcf res.vcf.gz # htslib command\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_file=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"4","hash":"ff\/b07fff","native_id":"30753325","process":"slivar_tsv","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/singularity\/gmillot-slivar_v2.0-gitlab_v9.1.img","tag":"-","name":"slivar_tsv","status":"COMPLETED","exit":"0","submit":"1664815010858","start":"1664815015798","complete":"1664815015813","duration":"4955","realtime":"3246","%cpu":"3.6","%mem":"0.0","rss":"5779456","vmem":"13815808","peak_rss":"5779456","peak_vmem":"13832192","rchar":"1034529","wchar":"686482","syscr":"293","syscw":"501","read_bytes":"2156544","write_bytes":"688128","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/ff\/b07ffffbb1620e9db94878651eb3d7","script":"\n #!\/bin\/bash -ue\n if [[ true == true ]] ; then \n slivar tsv --ped Dyslexia.pedigree.txt -s aff_only -i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only res.vcf > res.tsv\n gzip -f res.tsv \n fi\n ","scratch":"-","queue":"hubbioit","cpus":"1","memory":"64424509440","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p02\/ghfc_wgs_zeus\/WGS\/Dyslexia\/vcf\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz\nfun_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin\/slivar-functions.js\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nannot1_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/cadd-1.6-SNVs-phred10-GRCh37.zip\nannot2_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/gnomad-2.1.1-genome-GRCh37.zip\nsample_expr= \npedigree_expr=--family-expr \'aff_only:fam.every(find_het_aff_hom_ref_unaff)\'\nfilter=true\ntsv_file=true\ntsv_sample=aff_only\ntsv_info=-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only\nsystem_exec=slurm\nout_path_ini=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_slivar_1664813804\nqueue=hubbioit\nqos=--qos=hubbioit\nadd_options= \nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"64","inv_ctxt":"8"}], 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}; </script> diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/slivar-functions.js b/example of results/PL_family_WGS_slivar_1664813804/reports/slivar-functions.js similarity index 100% rename from example of results/PL_family_WGS_slivar_1664358140/reports/slivar-functions.js rename to example of results/PL_family_WGS_slivar_1664813804/reports/slivar-functions.js diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/slivar_vcf_extraction.config b/example of results/PL_family_WGS_slivar_1664813804/reports/slivar_vcf_extraction.config similarity index 97% rename from example of results/PL_family_WGS_slivar_1664358140/reports/slivar_vcf_extraction.config rename to example of results/PL_family_WGS_slivar_1664813804/reports/slivar_vcf_extraction.config index 26bc322..f371e91 100644 --- a/example of results/PL_family_WGS_slivar_1664358140/reports/slivar_vcf_extraction.config +++ b/example of results/PL_family_WGS_slivar_1664813804/reports/slivar_vcf_extraction.config @@ -30,6 +30,7 @@ env { sample_expr = " " // expression to use for the --sample-expr option of slivar. Example: sample_expr = "--sample-expr 'high_quality:sample.GQ >= 10'". Before the colon is the name of the new field added in the INFO field of the VCF. Write " " if no selection wanted (only annotation). "--sample-expr 'all:sample.DP >= 0'" Must be used if no filter wanted but tsv wanted. Another example: "--sample-expr 'all:sample.GQ == \".\"'" pedigree_expr = "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'" // expression to use for the --family-expr or --trio or --group-expr option of slivar in order to filter the data according to pedigree info or VCF info (depends on the .js file defined by fun_path above). See https://github.com/brentp/slivar#commands for details. Example: "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'". Write " " if no selection wanted (only annotation). Of note, for no filtering, pedigree_expr="all:fam.every(function(s){return s.affected || s.unaffected})" does not work, we have to use --sample-expr filter = "true" // if false, the output VCF is only labeled in the VCF INFO field according to the pedigree_expr parameter. If true, take only the labeled lines (variants) of the output VCF. Of note, true add the --pass-only argument to the slivar expr + tsv_file = "true" // if true, return a .tsv file of the .vcf file output tsv_sample = "aff_only" // mandatory -s option of the slivar tsv command. Example sample="aff_only". What is indicated must be a field of the INFO field of the vcf, added using the sample_expr or pedigree_expr parameter tsv_info = "-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only" // -i option of the slivar tsv command that extracts data from the INFO field of the vcf file (https://github.com/brentp/slivar#tsv) for the tsv file output. Example : "-i AC -i AF -i AN". Warning: if one of the -i is not in the vcf file, it will generate an error. Thus, be carefull with what is used in the sample_expr or pedigree_expr parameter } @@ -138,7 +139,7 @@ singularity { }else if(system_exec == 'slurm_local'){ cacheDir = 'singularity' // "$baseDir/singularity" can be used but do not forget double quotes. }else{ - cacheDir = '/mnt/c/Users/Gael/Documents/singularity' // "$baseDir/singularity" can be used but do not forget double quotes. + cacheDir = '/mnt/c/Users/gmillot/singularity' // "$baseDir/singularity" can be used but do not forget double quotes. } } @@ -170,7 +171,7 @@ process { } withLabel: slivar { - container='gmillot/slivar_v1.0:gitlab_v8.11' + container='gmillot/slivar_v2.0:gitlab_v9.1' cpus=1 memory='60G' } diff --git a/example of results/PL_family_WGS_slivar_1664358140/reports/timeline.html b/example of results/PL_family_WGS_slivar_1664813804/reports/timeline.html similarity index 99% rename from example of results/PL_family_WGS_slivar_1664358140/reports/timeline.html rename to example of results/PL_family_WGS_slivar_1664813804/reports/timeline.html index ec3530b..844b797 100644 --- a/example of results/PL_family_WGS_slivar_1664358140/reports/timeline.html +++ b/example of results/PL_family_WGS_slivar_1664813804/reports/timeline.html @@ -205,13 +205,15 @@ $(function() { // Nextflow report data window.data = { - "elapsed": "17m 41s", - "beginningMillis": 1664358140804, - "endingMillis": 1664359202028, + "elapsed": "20m 11s", + "beginningMillis": 1664813805109, + "endingMillis": 1664815016399, "processes": [ - {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1664358141685, "ending_time": 1664358146339}, {"starting_time": 1664358146339, "ending_time": 1664358146353, "label": "9.7s \/ 0"}, {"starting_time": 1664358146353, "ending_time": 1664358151345}]}, - {"label": "WorkflowVersion", "cached": false, "index": 1, "times": [{"starting_time": 1664358141744, "ending_time": 1664358146432}, {"starting_time": 1664358146432, "ending_time": 1664358146951, "label": "9.7s \/ 5.2 MB"}, {"starting_time": 1664358146951, "ending_time": 1664358151396}]}, - {"label": "slivar", "cached": false, "index": 2, "times": [{"starting_time": 1664358141799, "ending_time": 1664358151410}, {"starting_time": 1664358151410, "ending_time": 1664359202171, "label": "17m 40s \/ 2.2 GB"}]} + {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1664813805968, "ending_time": 1664813810695}, {"starting_time": 1664813810695, "ending_time": 1664813810749, "label": "4.7s \/ 0"}]}, + {"label": "WorkflowVersion", "cached": false, "index": 1, "times": [{"starting_time": 1664813806018, "ending_time": 1664813810762}, {"starting_time": 1664813810762, "ending_time": 1664813810903, "label": "4.8s \/ 0"}]}, + {"label": "slivar_extract", "cached": false, "index": 2, "times": [{"starting_time": 1664813990423, "ending_time": 1664813995703}, {"starting_time": 1664813995703, "ending_time": 1664815011821, "label": "17m \/ 2.2 GB"}]}, + {"label": "slivar_vcf_compress", "cached": false, "index": 3, "times": [{"starting_time": 1664815010820, "ending_time": 1664815015752}, {"starting_time": 1664815015752, "ending_time": 1664815015890, "label": "5s \/ 0"}]}, + {"label": "slivar_tsv", "cached": false, "index": 4, "times": [{"starting_time": 1664815010858, "ending_time": 1664815015798}, {"starting_time": 1664815015798, "ending_time": 1664815019044, "label": "5s \/ 5.5 MB"}]} ] } ; diff --git a/example of results/PL_family_WGS_slivar_1664813804/reports/trace.txt b/example of results/PL_family_WGS_slivar_1664813804/reports/trace.txt new file mode 100644 index 0000000..568c8d0 --- /dev/null +++ b/example of results/PL_family_WGS_slivar_1664813804/reports/trace.txt @@ -0,0 +1,6 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar +3 38/934009 30751438 Backup COMPLETED 0 2022-10-03 18:16:45.968 4.7s 54ms 7.2% 0 0 122.1 KB 1.5 KB +1 fc/31bb4d 30751439 WorkflowVersion COMPLETED 0 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See https://www.nextflow.io/docs/latest/config.html#scope-env env { - sample_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" // path of the sample file. Example : sample_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" sample_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz". The .tbi file seems not required when calling a .gz file + sample_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10.vcf" // path of the sample file. Example : sample_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" sample_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz". The .tbi file seems not required when calling a .gz file //Warning: do not write the out_path now. See below. If written here, the one below is not considered" fun_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/bin/slivar-functions.js" // .js file containing functions for the slivar --family-expr option. Example : fun_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/bin/slivar-functions.js", fun_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/bin/slivar-functions.js" ped_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.pedigree.txt" // path of the pedigree file. Example : ped_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/Dyslexia.pedigree.txt", ped_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // pedigree @@ -27,11 +27,12 @@ env { annot1_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/cadd-1.6-SNVs-phred10-GRCh37.zip" // path of the cadd annotation file. Example : annot1_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/cadd-1.6-SNVs-phred10-GRCh37.zip", annot1_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/references/GRCh37/slivar-gnotate/cadd-1.6-SNVs-phred10-GRCh37.zip" // cadd annotation annot2_path = "/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/gnomad-2.1.1-genome-GRCh37.zip" // path of gnomad annotation file. Example : annot2_path="/mnt/c/Users/Gael/Documents/Git_projects/slivar_vcf_extraction/dataset/gnomad-2.1.1-genome-GRCh37.zip", annot2_path="/pasteur/zeus/projets/p02/ghfc_wgs_zeus/references/GRCh37/slivar-gnotate/gnomad-2.1.1-genome-GRCh37.zip" // gnomad annotation - sample_expr = " " // expression to use for the --sample-expr option of slivar. Example: sample_expr = "--sample-expr 'high_quality:sample.GQ >= 10'". Before the colon is the name of the new field added in the INFO field of the VCF. Write " " if no selection wanted (only annotation). Write "--sample-expr 'all:true'" if no filter wanted but tsv wanted. Of note, "--sample-expr 'all:sample.GQ == \".\"'" is correctly written in the .command.sh file in the work dir of nextflow, but does not seem to work in selecting the empty GQ - pedigree_expr = "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'" // expression to use for the --family-expr or --trio or --group-expr option of slivar in order to filter the data according to pedigree info or VCF info (depends on the .js file defined by fun_path above). See https://github.com/brentp/slivar#commands for details. Example: "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'". Write " " if no selection wanted (only annotation). Of note, for no filtering, pedigree_expr="all:fam.every(function(s){return s.affected || s.unaffected})" does not work, we have to use --sample-expr - filter = "true" // if false, the output VCF is only labeled in the VCF INFO field according to the pedigree_expr parameter. If true, take only the labeled lines (variants) of the output VCF. Of note, true add the --pass-only argument to the slivar expr - tsv_sample = "aff_only" // mandatory -s option of the slivar tsv command. Example sample="aff_only". What is indicated must be a field of the INFO field of the vcf, added using the sample_expr or pedigree_expr parameter - tsv_info = "-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i aff_only" // -i option of the slivar tsv command that extracts data from the INFO field of the vcf file (https://github.com/brentp/slivar#tsv) for the tsv file output. Example : "-i AC -i AF -i AN". Warning: if one of the -i is not in the vcf file, it will generate an error. Thus, be carefull with what is used in the sample_expr or pedigree_expr parameter + sample_expr = "--sample-expr 'all:true'" // expression to use for the --sample-expr option of slivar. Example: sample_expr = "--sample-expr 'high_quality:sample.GQ >= 10'". Before the colon is the name of the new field added in the INFO field of the VCF. Write " " if no selection wanted (only annotation). Write "--sample-expr 'all:true'" if no filter wanted but tsv wanted. Warning: all:sample.DP >= 0 is not equivalent to all:true. Of note, "--sample-expr 'all:sample.GQ == \".\"'" is correctly written in the .command.sh file in the work dir of nextflow, but does not seem to work in selecting the empty GQ + pedigree_expr = " " // expression to use for the --family-expr or --trio or --group-expr option of slivar in order to filter the data according to pedigree info or VCF info (depends on the .js file defined by fun_path above). See https://github.com/brentp/slivar#commands for details. Example: "--family-expr 'aff_only:fam.every(find_het_aff_hom_ref_unaff)'". Write " " if no selection wanted (only annotation). Of note, for no filtering, pedigree_expr="all:fam.every(function(s){return s.affected || s.unaffected})" does not work, we have to use --sample-expr + filter = "false" // if false, the output VCF is only labeled in the VCF INFO field according to the pedigree_expr parameter. If true, take only the labeled lines (variants) of the output VCF. Of note, true add the --pass-only argument to the slivar expr + tsv_file = "true" // if true, return a .tsv file of the .vcf file output + tsv_sample = "all" // mandatory -s option of the slivar tsv command. Example sample="aff_only". What is indicated must be a field of the INFO field of the vcf, added using the sample_expr or pedigree_expr parameter. Ignored if tsv_file == "true" + tsv_info = "-i AC -i AF -i AN -i BaseQRankSum -i DB -i DP -i ExcessHet -i FS -i InbreedingCoeff -i MLEAC -i MLEAF -i MQ -i MQRankSum -i QD -i ReadPosRankSum -i SOR -i VQSLOD -i culprit -i CSQ -i cadd_phred -i gno_non_neuro_af_all -i gno_non_neuro_af_nfe -i gno_non_neuro_nhomalt_all -i gno_non_neuro_nhomalt_nfe -i highest_impact_order -i all" // -i option of the slivar tsv command that extracts data from the INFO field of the vcf file (https://github.com/brentp/slivar#tsv) for the tsv file output. Example : "-i AC -i AF -i AN". Warning: if one of the -i is not in the vcf file, it will generate an error. Thus, be carefull with what is used in the sample_expr or pedigree_expr parameter. Ignored if tsv_file == "true" } //////// end variables that will be used only in the main.nf @@ -169,7 +170,7 @@ process { } withLabel: slivar { - container='gmillot/slivar_v1.0:gitlab_v8.11' + container='gmillot/slivar_v2.0:gitlab_v9.1' cpus=1 memory='60G' } diff --git a/slivar_vcf_extraction.nf b/slivar_vcf_extraction.nf index 2824993..2ec34c6 100644 --- a/slivar_vcf_extraction.nf +++ b/slivar_vcf_extraction.nf @@ -72,8 +72,11 @@ if( ! sample_expr in String ){ if( ! pedigree_expr in String ){ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID pedigree_expr PARAMETER IN nextflow.config FILE:\n${pedigree_expr}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n" } -if( ! filter in String ){ - error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID filter PARAMETER IN nextflow.config FILE:\n${filter}\nMUST BE THE SINGLE CHARACTER STRING true OR false\n\n========\n\n" +if( ! (filter == "true" || filter == "false")){ + error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID filter PARAMETER IN nextflow.config FILE:\n${filter}\nMUST BE THE SINGLE CHARACTER STRING \"true\" OR \"false\"\n\n========\n\n" +} +if( ! (tsv_file == "true" || tsv_file == "false")){ + error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID tsv_file PARAMETER IN nextflow.config FILE:\n${tsv_file}\nMUST BE THE SINGLE CHARACTER STRING \"true\" OR \"false\"\n\n========\n\n" } if( ! tsv_sample in String ){ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID tsv_sample PARAMETER IN nextflow.config FILE:\n${tsv_sample}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n" @@ -145,10 +148,10 @@ process WorkflowVersion { // create a file with the workflow version in out_path -process slivar { +process slivar_extract { label 'slivar' // see the withLabel: bash in the nextflow config file - publishDir path: "${out_path}", mode: 'copy', overwrite: false - cache 'false' + //publishDir path: "${out_path}", mode: 'copy', overwrite: false + cache 'true' //no channel input here for the vcf, because I do not transform it input: @@ -160,25 +163,71 @@ process slivar { val sample_expr val pedigree_expr val filter + // see the scope for the use of affected_patients which is already a variable from .config file + + output: + file "res.vcf" into vcf_ch1, vcf_ch2 + + script: + """ + #!/bin/bash -ue + slivar expr --js ${fun} -g ${annot1} -g ${annot2} --vcf ${vcf} --ped ${ped} ${sample_expr} ${pedigree_expr} ${filter} -o "res.vcf" + """ + // write ${} between "" to make a single argument when the variable is made of several values separated by a space. Otherwise, several arguments will be considered +} + + +process slivar_tsv { + label 'slivar' // see the withLabel: bash in the nextflow config file + publishDir path: "${out_path}", mode: 'copy', overwrite: false + cache 'true' + + //no channel input here for the vcf, because I do not transform it + input: + file vcf from vcf_ch1 + file ped + val tsv_file val tsv_sample val tsv_info // see the scope for the use of affected_patients which is already a variable from .config file output: - file "res.vcf" - file "res.tsv" + file "res.*" optional true + script: """ #!/bin/bash -ue - - # add the modification of the pedigree if - slivar expr --js ${fun} -g ${annot1} -g ${annot2} --vcf ${vcf} --ped ${ped} ${sample_expr} ${pedigree_expr} ${filter} -o "res.vcf" - slivar tsv --ped ${ped} -s ${tsv_sample} ${tsv_info} res.vcf > res.tsv + if [[ ${tsv_file} == true ]] ; then + slivar tsv --ped ${ped} -s ${tsv_sample} ${tsv_info} ${vcf} > res.tsv + gzip -f res.tsv + fi """ // write ${} between "" to make a single argument when the variable is made of several values separated by a space. Otherwise, several arguments will be considered } +process slivar_vcf_compress { + label 'slivar' // see the withLabel: bash in the nextflow config file + publishDir path: "${out_path}", mode: 'copy', overwrite: false + cache 'true' + + //no channel input here for the vcf, because I do not transform it + input: + file vcf from vcf_ch2 + // see the scope for the use of affected_patients which is already a variable from .config file + + output: + file "res.*" + + + script: + """ + #!/bin/bash -ue + bgzip -cf -l 9 ${vcf} > res.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking + tabix -p vcf res.vcf.gz # htslib command + """ + // write ${} between "" to make a single argument when the variable is made of several values separated by a space. Otherwise, several arguments will be considered +} -- GitLab