Commit 8f823aa5 authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Improved export for volcano plot, debug diversity confidence interval

parent 060f7c9b
Pipeline #34434 failed with stages
in 50 minutes and 39 seconds
......@@ -38,10 +38,10 @@ RUN wget --no-verbose https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz -P
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb && \
wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201909.tar.gz -P /opt && \
wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202007.tar.gz -P /opt && \
mkdir /opt/packman
RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_201909.tar.gz', '/opt/packman')"""
RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_202007.tar.gz', '/opt/packman')"""
COPY docker_inst/shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY docker_inst/.Rprofile /srv/shiny-server/
......
......@@ -50,13 +50,13 @@ chmod +x ./shaman/www/shaman.R && Rscript ./shaman/www/shaman.R
SHAMAN is available for R=3.6.1. Packrat framework allows an easy installation of all the dependencies. Of note, raw data submission is not possible with this version.
```
# Download packrat package
wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz
wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202007.tar.gz
mkdir packrat/shaman
```
Now you can run R:
```
install.packages("packrat")
packrat::unbundle("shaman_package_201908.tar.gz", "packrat/shaman")
packrat::unbundle("shaman_package_202007.tar.gz", "packrat/shaman")
packrat::init("packrat/shaman")
system("Rscript -e 'shiny::runGitHub("pierreLec/KronaRShy",port=5438)'",wait=FALSE),
shiny::runGitHub('aghozlane/shaman')
......
......@@ -209,7 +209,7 @@ Volcano_Plot <- function(input, data, export = FALSE) {
axis.text = element_text(size = input$axisFontSize),
legend.title = element_text(size = input$axisFontSize),
legend.text = element_text(size = input$axisFontSize))
plot <- plot + geom_text(aes(label = labels, color = color_var), size = input$labelsSize %/% 3, hjust = 1, vjust = 1, show.legend = FALSE)
plot <- plot + geom_text_repel(aes(label = labels, color = color_var), size = input$labelsSize %/% 3, hjust = 1, vjust = 1, show.legend = FALSE)
plot <- plot + scale_color_manual(name = "Group", values = c("Down" = input$colour1,"Not significant" = input$colour2,"Up" = input$colour3))
if(input$showSignifThresholds){
plot <- plot + geom_hline(yintercept = y_signif, linetype = "dashed", size = input$signifThresholdsWidth/2)
......
......@@ -450,32 +450,32 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE, alpha_transparen
alpha=alpha[alpha_selected]
alpha_sd = tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, sd)
alpha_sd=alpha_sd[alpha_selected]
ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb[alpha_selected],0)
ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb[alpha_selected]
ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb,0)
ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb
shan <- tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, mean)
shan_selected = !is.na(shan)
shan = shan[shan_selected]
shan_sd = tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, sd)
shan_sd = shan_sd[shan_selected]
ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb[shan_selected],0)
ci.shan.up = shan + 1.96*shan_sd/sqrt.nb[shan_selected]
ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb,0)
ci.shan.up = shan + 1.96*shan_sd/sqrt.nb
simpson <- tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, mean)
simpson_selected = !is.na(simpson)
simpson = simpson[simpson_selected]
simpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, sd)
simpson_sd = simpson_sd[simpson_selected]
ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb[simpson_selected],0)
ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb[simpson_selected]
ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb,0)
ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb
invsimpson <- tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, mean)
invsimpson_selected = !is.na(invsimpson)
invsimpson = invsimpson[invsimpson_selected]
invsimpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, sd)
invsimpson_sd = invsimpson_sd[invsimpson_selected]
ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected],0)
ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected]
ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb,0)
ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb
gamma <- TaxoNumber(counts_tmp_combined, targetInt$AllVar)
gamma = gamma[!is.na(gamma)]
......
{"type": "16S", "path_R2": "/tmp/Rtmp6ySBtN/Masque_files_R2", "phredthres": 0, "annotationstrand": "both", "aFmax": 0.945, "aPmin": 0.75, "aSmin": 0.98, "aKmin": 0.75, "minreadlength": 50, "mail": "amine.ghozlane@pasteur.fr", "clusteringthreshold": 0.97, "aOmax": 0.865, "contaminant": "/tmp/Rtmp6ySBtN/filea1a9748bebd0_contaminant.fasta", "name": "filea1a9748bebd0", "pattern_R1": "_L001_R1_001", "clusteringstrand": "both", "aCmin": 0.785, "minampliconlength": 50, "aPmax": 0.785, "dreptype": "--derep_prefix", "maxampliconlength": 0, "data_history_name": "data_shaman_2186_106", "minoverlap": 10, "aOmin": 0.82, "aGmin": 0.945, "path_R1": "/tmp/Rtmp6ySBtN/Masque_files_R1", "aFmin": 0.865, "paired": true, "result_history_name": "shaman_2186_106", "mincorrect": 50, "minabundance": 4, "host": "", "aGmax": 0.98, "aCmax": 0.82}
\ No newline at end of file
This diff is collapsed.
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_15 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_45 Bacteria Cyanobacteria 4C0d-2 MLE1-12
OTU_14 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae
OTU_4 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_20 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae
OTU_19 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_25 Bacteria Firmicutes
OTU_1 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_42 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_70 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_59 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae
OTU_60 Bacteria Firmicutes Bacilli Gemellales
OTU_67 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_46 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_65 Bacteria Fusobacteria Fusobacteriia Fusobacteriales Leptotrichiaceae Sneathia
OTU_44 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7
OTU_18 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella
OTU_49 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_66 Bacteria Firmicutes Bacilli Lactobacillales
OTU_40 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_38 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_2 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_11 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae
OTU_24 Bacteria Actinobacteria Actinobacteria Actinomycetales Propionibacteriaceae Propionibacterium acnes
OTU_6 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_5 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_69 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_43 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_53 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_3 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_47 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_61 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_9 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_12 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_55 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_62 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_26 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_28 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_7 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_52 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
(OTU_43:0.042884653,(OTU_4:0.000000007,OTU_46:0.009390584)0.912:0.017870958,(OTU_49:0.020821676,(OTU_47:0.022300505,((((OTU_66:0.000000007,(OTU_61:0.045356270,((OTU_69:0.000000007,OTU_60:0.039062501)0.731:0.000000007,(OTU_2:0.000000007,OTU_38:0.030038757)0.860:0.000000006)0.799:0.010322779)0.999:0.054793408)0.995:0.037939994,((OTU_40:0.036746419,(OTU_3:0.000000006,OTU_15:0.048600555)0.730:0.002422572)0.992:0.052006245,(((OTU_28:0.000000006,((((OTU_8:0.000000007,OTU_26:0.039668158)0.992:0.058171794,(((OTU_44:0.431891816,OTU_20:0.087273420)0.842:0.074934215,((OTU_45:0.225427475,OTU_24:0.213406872)0.972:0.107393644,(OTU_65:0.323090252,OTU_59:0.128938744)0.903:0.053503914)0.469:0.044803896)0.256:0.046064093,((OTU_5:0.000000007,OTU_18:0.046264531)0.974:0.058184509,(OTU_6:0.000000007,OTU_19:0.045890322)0.797:0.017831029)0.997:0.101410042)0.969:0.067883746)0.990:0.062039729,(OTU_14:0.000000007,(((OTU_62:0.001400378,(OTU_9:0.000000007,OTU_25:0.000000007)0.949:0.068063487)0.903:0.054124751,OTU_55:0.002770174)0.830:0.013064319,OTU_12:0.041163336)1.000:0.083967902)0.963:0.043561117)1.000:0.085639968,OTU_11:0.000000007)1.000:0.127315011)0.999:0.046124874,(OTU_1:0.000000007,OTU_42:0.042015878)0.765:0.000000006)0.971:0.037307077,OTU_70:0.015826282)1.000:0.099109147)0.308:0.013182076)0.921:0.019086489,(OTU_7:0.000000006,(OTU_52:0.018102916,OTU_53:0.020976946)0.985:0.024227705)0.903:0.015356962)0.924:0.026938270,OTU_67:0.000000006)0.993:0.029424143)0.900:0.011283368)0.872:0.013708432);
This diff is collapsed.
#OTU ID 1ng-25cycles-1_S38 1ng-25cycles-2_S39 1ng-25cycles-3_S40 1ng-30cycles-1_S50 1ng-30cycles-2_S51 1ng-30cycles-3_S52 20ng-20cycles-1_S14 20ng-20cycles-2_S15 20ng-20cycles-3_S16 20ng-25cycles-1_S2 20ng-25cycles-2_S3 20ng-25cycles-3_S4 5ng-25cycles-1_S26 5ng-25cycles-2_S27 5ng-25cycles-3_S28 zero5ng-25cycles-1_S62 zero5ng-25cycles-2_S63 zero5ng-25cycles-3_S64 zero5ng-30cycles-1_S74 zero5ng-30cycles-2_S75 zero5ng-30cycles-3_S76
OTU_1 20360 31734 26239 39341 51068 34607 43387 51788 45285 45424 38082 46877 29728 34067 36653 43241 45307 31809 49944 29197 12686
OTU_10 15 0 12 23 4 6 20 20 12 25 1 12 40 0 25 23 4 16 50 8 5
OTU_11 31 41 19 107 104 55 46 44 33 107 137 82 43 63 44 18 27 20 138 61 18
OTU_12 81 146 101 305 409 193 177 233 141 336 403 350 167 239 182 128 186 92 378 243 54
OTU_13 8 5 18 40 8 6 30 27 20 33 1 22 50 6 54 18 0 24 62 19 4
OTU_14 33 81 36 181 210 103 57 103 59 183 211 175 106 123 112 61 93 26 248 189 24
OTU_15 24 77 27 101 174 79 39 76 57 100 133 103 66 49 50 52 77 35 71 102 19
OTU_16 3 1 3 32 1 2 14 11 1 11 8 9 16 7 21 6 1 9 10 13 4
OTU_17 0 2 0 4 4 0 6 3 2 5 3 1 1 2 6 1 0 2 9 5 0
OTU_18 24 47 39 86 129 54 35 80 60 82 121 96 38 88 85 53 71 28 85 57 8
OTU_19 12 37 15 60 83 53 41 54 22 63 91 77 55 70 49 20 49 22 66 59 7
OTU_2 18676 27903 26126 34853 50574 32174 42742 55406 45490 37495 29397 35607 30330 40305 37747 45089 50059 35897 46262 33097 9973
OTU_20 0 7 4 10 11 10 0 0 0 0 0 0 0 3 0 14 20 5 16 6 0
OTU_21 3 1 1 20 5 2 4 6 11 2 8 10 8 8 4 2 3 2 13 6 3
OTU_22 0 0 0 0 5 1 1 0 2 1 0 5 5 0 0 0 1 1 8 0 1
OTU_23 5 0 0 4 5 0 0 2 2 4 0 7 5 1 1 0 0 2 5 0 0
OTU_24 2 4 4 13 5 4 0 0 1 0 1 0 0 2 2 18 6 2 16 8 4
OTU_25 2 1 1 3 6 1 0 2 1 3 6 6 0 2 7 0 0 0 5 3 0
OTU_26 26 61 23 103 136 69 30 85 72 114 104 102 50 89 98 43 63 37 120 67 14
OTU_27 0 0 5 2 0 0 0 2 2 1 0 2 0 0 0 2 0 0 3 0 0
OTU_28 12 18 13 39 60 38 15 25 22 61 41 54 22 41 16 13 33 6 63 21 9
OTU_29 0 0 0 3 0 2 0 3 9 2 0 0 4 0 1 4 0 0 2 3 0
OTU_3 15314 25794 20477 27080 42310 25483 35798 49896 38160 29170 26927 30129 24028 32206 32946 37830 44979 31431 35228 26258 7556
OTU_30 0 2 0 2 0 0 0 0 0 2 0 3 0 0 1 0 0 0 6 0 0
OTU_31 2 0 1 1 0 0 0 3 1 1 2 0 0 5 2 0 0 2 0 0 0
OTU_32 0 0 0 0 3 0 5 1 0 2 0 2 0 0 0 2 0 0 2 0 0
OTU_33 2 1 0 0 0 1 5 1 2 7 0 1 2 5 0 1 2 2 8 6 1
OTU_34 2 3 0 2 0 2 1 2 0 1 0 1 0 0 0 0 0 2 2 0 0
OTU_35 0 0 1 2 0 0 3 3 3 1 2 1 5 2 0 1 0 0 6 3 0
OTU_36 1 0 0 3 0 0 0 0 2 0 0 2 1 1 2 1 4 2 2 5 0
OTU_37 0 0 0 3 0 1 0 0 0 0 0 2 0 2 0 1 0 0 1 2 0
OTU_38 18 49 21 76 100 69 42 57 37 92 102 72 55 87 75 33 69 20 91 65 16
OTU_39 0 3 0 0 0 0 0 0 0 0 4 1 0 0 1 2 0 0 4 0 0
OTU_4 16885 29352 20248 35722 51543 31124 43834 49443 39468 39295 32315 31447 31638 39818 43126 48856 47605 32203 48057 32531 7283
OTU_40 34 71 39 152 211 70 92 144 72 129 144 113 90 124 126 80 109 60 197 91 28
OTU_41 1 0 0 1 0 1 0 2 0 1 0 0 0 0 1 2 0 0 0 0 0
OTU_42 122 234 132 459 646 276 214 352 261 426 501 439 250 410 337 201 335 118 554 346 88
OTU_43 3 8 2 24 21 15 3 9 6 48 33 20 15 6 13 6 3 0 28 19 7
OTU_44 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 3 4 0 12 0
OTU_45 0 0 0 0 1 0 0 0 0 0 0 0 3 3 0 0 0 0 5 3 0
OTU_46 1 2 2 4 7 1 5 0 0 0 6 0 0 1 7 1 4 1 2 4 0
OTU_47 251 434 240 910 1133 514 426 752 465 976 922 818 459 718 581 386 562 280 1158 758 51
OTU_48 1 0 0 0 0 0 2 2 0 0 0 0 0 0 0 3 0 0 0 0 0
OTU_49 286 510 294 1191 1456 598 540 800 498 1240 1044 1044 597 1024 748 435 610 315 1447 815 77
OTU_5 14126 24363 19543 28630 43085 22741 32492 43287 35159 32594 29854 35222 24098 33055 33176 33168 40478 29085 38149 27187 3814
OTU_50 0 0 0 0 0 0 0 0 0 5 0 0 0 0 1 1 0 0 0 0 0
OTU_51 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 0 0
OTU_52 38 59 28 107 107 54 71 89 47 98 95 118 61 88 70 40 51 20 151 92 7
OTU_53 79 157 90 345 430 135 164 269 147 350 316 307 175 259 193 112 211 95 435 250 21
OTU_54 0 0 0 2 0 0 0 0 0 0 0 2 3 0 1 0 0 1 1 0 0
OTU_55 43 93 43 179 237 168 107 140 120 241 250 230 129 169 142 88 152 47 231 165 24
OTU_56 0 0 2 0 0 1 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0
OTU_57 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3 0 0 0 0 1
OTU_58 0 0 0 0 2 0 0 0 0 4 0 2 0 0 0 1 0 0 0 2 0
OTU_59 0 0 3 1 0 0 0 0 0 0 0 0 0 0 0 6 1 2 6 2 1
OTU_6 10221 17184 13612 20142 30222 18339 22934 29582 23374 22158 21126 24194 16763 22817 21790 23266 28458 18470 26889 19066 5882
OTU_60 52 69 40 147 235 118 81 135 97 152 160 189 109 146 88 54 98 44 191 136 50
OTU_61 5 10 0 24 19 13 7 6 3 20 22 15 6 14 15 2 6 0 38 13 6
OTU_62 23 94 38 137 188 107 58 89 80 189 143 141 83 130 97 61 75 34 149 123 20
OTU_63 0 0 0 0 0 0 0 1 0 2 0 0 1 0 1 0 0 2 0 0 0
OTU_64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0
OTU_65 0 0 2 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
OTU_66 104 191 79 439 444 250 168 311 180 365 390 277 203 285 269 139 249 72 427 262 80
OTU_67 128 216 117 407 543 262 223 311 203 420 398 352 209 278 343 194 282 118 471 296 71
OTU_68 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
OTU_69 3 2 1 10 9 9 9 9 3 10 8 9 2 10 2 5 9 3 15 7 8
OTU_7 7592 13857 9387 13681 22111 12021 16756 22535 17609 15537 14537 15067 10473 14958 15970 17494 21041 13521 17356 13458 4075
OTU_70 4 4 3 43 32 16 1 10 1 37 24 20 3 16 8 5 1 1 30 18 2
OTU_8 6475 11438 8766 13541 20838 9719 15078 22324 17257 14658 14653 16586 11792 16048 16112 14737 19042 11961 19486 13319 1717
OTU_9 71 128 63 222 340 161 129 167 103 274 275 208 130 238 183 120 143 68 318 224 39
Type Count Mean_length Median_length
Amplicon 5667037 429 427
Dereplication 2807991 429 427
Singleton_removed 41960 430 427
Chimera_removed 35606 430 427
OTU 70 353 424
silva_annotation 42
greengenes_annotation 41
rdp_annotation 69
sample Raw_reads_fwd Raw_mean_length_fwd Raw_median_length_fwd Raw_reads_rev Raw_mean_length_rev Raw_median_length_rev Trimmed Trimmed_fwd Trimmed_rev Removed Removed_fwd Removed_rev Filtered_reads_fwd Filtered_mean_length_fwd Filtered_median_length_fwd Filtered_reads_rev Filtered_mean_length_rev Filtered_median_length_rev Combined pairs Uncombined pairs Selected_dereplication Selected_singleton Selected_chimera Selected_otu Mapped_reads Mapping_percent_combined
5ng-25cycles-2_S27 284620 300 301 284620 300 300 535653 251625 284028 14 7 7 284613 285 284 284613 279 279 282525 284613 131359 2125 1756 4 238088 83.65
20ng-20cycles-1_S14 297586 300 301 297586 300 300 561759 264767 296992 4 2 2 297584 285 284 297584 279 279 295212 297584 134679 2100 1886 4 255895 85.99
20ng-25cycles-3_S4 296908 300 301 296908 300 300 564512 268252 296260 8 4 4 296904 285 284 296904 279 279 294155 296904 141106 2246 1812 5 240633 81.05
5ng-25cycles-1_S26 216807 300 301 216807 300 300 410968 194591 216377 6 3 3 216804 285 284 216804 279 279 215222 216804 98761 1547 1296 6 182120 84.0
20ng-25cycles-1_S2 302678 300 301 302678 300 300 577044 274979 302065 13 7 6 302671 285 284 302671 279 279 299987 302671 148426 2291 1814 3 242561 80.14
zero5ng-25cycles-2_S63 352123 300 301 352123 300 300 659554 308094 351460 4 2 2 352121 286 284 352121 279 279 348756 352121 165806 2592 2317 2 300582 85.36
zero5ng-25cycles-1_S62 308283 300 301 308283 300 300 581421 273749 307672 6 3 3 308280 285 284 308280 279 279 305526 308280 140665 2110 1940 2 266145 86.33
1ng-25cycles-2_S39 225513 300 301 225513 300 300 422683 197695 224988 4 2 2 225511 286 284 225511 279 279 222725 225511 116008 1826 1583 3 184494 81.81
1ng-30cycles-1_S50 275152 300 301 275152 300 300 520299 245752 274547 34 17 17 275134 285 284 275134 279 279 272693 275134 136424 2068 1587 8 219023 79.61
20ng-25cycles-2_S3 269896 300 301 269896 300 300 510908 241591 269317 8 4 4 269892 285 284 269892 279 279 267249 269892 135359 2156 1676 2 213001 78.92
1ng-25cycles-1_S38 133794 300 301 133794 300 300 252331 118843 133488 4 2 2 133792 285 284 133792 279 279 132305 133792 66824 1033 915 2 111204 83.12
zero5ng-25cycles-3_S64 236495 300 301 236495 300 300 445831 209795 236036 5 3 2 236492 285 284 236492 279 279 234247 236492 104951 1692 1581 3 206026 87.12
20ng-20cycles-2_S15 386487 300 301 386487 300 300 727489 341766 385723 10 5 5 386482 285 284 386482 279 279 383237 386482 179798 2840 2514 2 328702 85.05
zero5ng-30cycles-3_S76 132333 300 301 132333 300 300 244174 114554 129620 2 1 1 132332 286 284 132332 280 279 118610 132332 110832 428 383 0 53758 40.62
1ng-25cycles-3_S40 172137 300 301 172137 300 300 324738 152947 171791 2 1 1 172136 285 284 172136 279 279 170386 172136 83061 1292 1175 4 145965 84.8
zero5ng-30cycles-2_S75 242911 300 301 242911 300 300 461139 218777 242362 14 7 7 242904 285 284 242904 279 279 240422 242904 113875 1744 1430 4 198702 81.8
zero5ng-30cycles-1_S74 359368 300 301 359368 300 300 682671 324017 358654 45 23 22 359345 285 284 359345 279 279 355985 359345 172641 2623 2030 5 288718 80.35
20ng-20cycles-3_S16 306702 300 301 306702 300 300 578443 272408 306035 6 3 3 306699 285 284 306699 279 279 303921 306699 135634 2066 1881 1 264662 86.29
1ng-30cycles-2_S51 391843 300 301 391843 300 300 739590 348609 390981 10 5 5 391838 285 284 391838 279 279 388256 391838 191024 3020 2504 4 319274 81.48
5ng-25cycles-3_S28 285903 300 301 285903 300 300 540819 255475 285344 4 2 2 285901 285 284 285901 279 279 283559 285901 127824 1980 1635 4 241584 84.5
1ng-30cycles-3_S52 256766 300 301 256766 300 300 481510 225448 256062 6 3 3 256763 286 284 256763 279 279 252059 256763 172934 2181 1891 2 189728 73.89
This diff is collapsed.
This diff is collapsed.
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_25 Bacteria Firmicutes
OTU_59 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp.
OTU_40 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria
OTU_9 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_62 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella
OTU_60 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Fastidiosipila
OTU_2 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_5 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella Salmonella enterica subsp. enterica serovar Agona str. 47.E.09
OTU_45 Bacteria Cyanobacteria Melainabacteria Obscuribacterales
OTU_44 Bacteria Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae
OTU_19 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella
OTU_20 Bacteria Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas uncultured Comamonadaceae bacterium
OTU_3 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Listeria monocytogenes
OTU_47 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria
OTU_14 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae
OTU_70 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_18 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella
OTU_4 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_65 Bacteria Fusobacteria Fusobacteriia Fusobacteriales Leptotrichiaceae Sneathia
OTU_8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_67 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_6 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella Escherichia coli
OTU_66 Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae Granulicatella
OTU_11 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae
OTU_28 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_49 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_15 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria
OTU_1 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus Lactobacillus sp. 2011_Ileo_VSA_C5
OTU_26 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_41 Eukaryota Fungi Tremellomycetes Tremellales Cryptococcaceae Cryptococcus Cryptococcus neoformans var. neoformans B-3501A
OTU_69 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_12 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae
OTU_55 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae
OTU_61 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_7 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus Enterococcus faecalis
OTU_24 Bacteria Actinobacteria Actinobacteria Propionibacteriales Propionibacteriaceae Cutibacterium Cutibacterium acnes
OTU_46 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_53 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_52 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_38 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus
OTU_43 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_42 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
(OTU_43:0.043065538,(OTU_4:0.000000007,OTU_46:0.009499885)0.925:0.018605697,(OTU_49:0.020643917,(((OTU_40:0.036758939,(OTU_3:0.000000007,OTU_15:0.049180884)0.733:0.002875830)0.991:0.039579799,((OTU_66:0.017902335,(OTU_61:0.050068509,((OTU_69:0.000000007,OTU_60:0.039615642)0.000:0.000000007,(OTU_2:0.000000007,OTU_38:0.030429043)0.000:0.000000007)0.705:0.006231766)0.986:0.041162159)0.000:0.029462530,(((OTU_14:0.000000007,(((OTU_8:0.000000007,OTU_26:0.039942502)0.988:0.056796602,((OTU_20:0.146385742,((OTU_65:0.326111890,OTU_59:0.133033691)0.882:0.051081053,(OTU_44:0.414762963,(OTU_45:0.236062817,OTU_24:0.201453677)0.514:0.045175108)0.901:0.080591364)0.201:0.041178794)0.912:0.057034587,((OTU_5:0.000000006,OTU_18:0.046682783)0.975:0.058197730,(OTU_6:0.000000007,OTU_19:0.046385742)0.804:0.018453808)0.997:0.102953636)0.974:0.067491668)0.992:0.065261015,OTU_11:0.086703754)0.882:0.043661284)0.872:0.050119101,(_R_OTU_41:1.823998631,(((OTU_62:0.002081216,(OTU_9:0.000000007,OTU_25:0.000000007)0.950:0.068029812)0.971:0.053834779,OTU_55:0.003022945)0.646:0.006742090,OTU_12:0.047049095)0.000:0.021518168)0.557:0.021182743)1.000:0.177012761,(OTU_70:0.000000007,(OTU_28:0.046271013,(OTU_1:0.000000007,OTU_42:0.042679568)0.000:0.000000007)0.993:0.051799927)0.996:0.088730473)0.551:0.021344639)0.895:0.026850633)0.646:0.032331834,((OTU_67:0.000000007,(OTU_7:0.000000007,(OTU_52:0.018211514,OTU_53:0.021321050)0.987:0.024554344)1.000:0.041446735)0.995:0.030584891,OTU_47:0.022411077)0.000:0.000000007)0.873:0.011411699)0.848:0.014281058);
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment