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

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
OTU_1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 1.0 Lactobacillaceae family 1.0 Lactobacillus genus 1.0
OTU_2 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_3 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 1.0 Listeria genus 1.0
OTU_4 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.99 Bacillus genus 0.99
OTU_5 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 1.0
OTU_6 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Escherichia/Shigella genus 1.0
OTU_7 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 1.0 Enterococcaceae family 1.0 Enterococcus genus 1.0
OTU_8 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 Pseudomonadales order 1.0 Pseudomonadaceae family 1.0 Pseudomonas genus 1.0
OTU_9 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.76 Gammaproteobacteria class 0.76 "Enterobacteriales" order 0.74 Enterobacteriaceae family 0.74 Leclercia genus 0.54
OTU_10 - Root rootrank 1.0 Bacteria domain 0.97 Firmicutes phylum 0.17 Negativicutes class 0.06 Selenomonadales order 0.06 Veillonellaceae family 0.06 Thermosinus genus 0.04
OTU_11 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.64 Gammaproteobacteria class 0.64 Pseudomonadales order 0.61 Pseudomonadaceae family 0.61 Thiopseudomonas genus 0.3
OTU_12 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.66 Gammaproteobacteria class 0.66 "Enterobacteriales" order 0.64 Enterobacteriaceae family 0.64 Leclercia genus 0.45
OTU_13 - Root rootrank 1.0 Bacteria domain 0.94 Firmicutes phylum 0.21 Clostridia class 0.15 Halanaerobiales order 0.09 Halanaerobiaceae family 0.09 Halothermothrix genus 0.09
OTU_14 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.5 Gammaproteobacteria class 0.5 Pseudomonadales order 0.49 Pseudomonadaceae family 0.49 Thiopseudomonas genus 0.23
OTU_15 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 1.0 Listeria genus 1.0
OTU_16 Root rootrank 1.0 Archaea domain 0.27 "Crenarchaeota" phylum 0.2 Thermoprotei class 0.2 Thermoproteales order 0.19 Thermoproteaceae family 0.19 Thermocladium genus 0.18
OTU_17 - Root rootrank 1.0 Archaea domain 0.21 "Euryarchaeota" phylum 0.2 Thermoplasmata class 0.18 Methanomassiliicoccales order 0.18 Methanomassiliicoccaceae family 0.18 Methanomassiliicoccus genus 0.18
OTU_18 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 0.58
OTU_19 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Escherichia/Shigella genus 1.0
OTU_20 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Betaproteobacteria class 1.0 Burkholderiales order 1.0 Comamonadaceae family 1.0 Pelomonas genus 1.0
OTU_21 - Root rootrank 1.0 Archaea domain 0.23 Pacearchaeota phylum 0.05 Pacearchaeota Incertae Sedis AR13 genus 0.05
OTU_22 Root rootrank 1.0 Bacteria domain 0.92 "Synergistetes" phylum 0.11 Synergistia class 0.11 Synergistales order 0.11 Synergistaceae family 0.11 Jonquetella genus 0.09
OTU_23 Root rootrank 1.0 Bacteria domain 0.82 "Bacteroidetes" phylum 0.42 "Bacteroidia" class 0.14 "Bacteroidales" order 0.14 "Bacteroidales"_incertae_sedis family 0.1 Phocaeicola genus 0.1
OTU_24 Root rootrank 1.0 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Actinobacteridae subclass 1.0 Actinomycetales order 1.0 Propionibacterineae suborder 1.0 Propionibacteriaceae family 1.0 Propionibacterium genus 1.0
OTU_25 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 0.73 Bacilli class 0.71 Bacillales order 0.68 Bacillaceae 2 family 0.62 Allobacillus genus 0.22
OTU_26 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 Pseudomonadales order 1.0 Pseudomonadaceae family 1.0 Pseudomonas genus 0.68
OTU_27 Root rootrank 1.0 Archaea domain 0.35 "Euryarchaeota" phylum 0.13 Methanopyri class 0.03 Methanopyrales order 0.03 Methanopyraceae family 0.03 Methanopyrus genus 0.03
OTU_28 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 0.99 Lactobacillales order 0.99 Lactobacillaceae family 0.97 Lactobacillus genus 0.97
OTU_29 - Root rootrank 1.0 Bacteria domain 0.81 "Deinococcus-Thermus" phylum 0.07 Deinococci class 0.07 Thermales order 0.06 Thermaceae family 0.06 Marinithermus genus 0.06
OTU_30 Root rootrank 1.0 Bacteria domain 0.92 "Lentisphaerae" phylum 0.04 Oligosphaeria class 0.04 Oligosphaerales order 0.04 Oligosphaeraceae family 0.04 Oligosphaera genus 0.04
OTU_31 Root rootrank 1.0 Bacteria domain 0.75 "Proteobacteria" phylum 0.34 Gammaproteobacteria class 0.28 Gammaproteobacteria_incertae_sedis order 0.19 Candidatus Carsonella genus 0.19
OTU_32 Root rootrank 1.0 Bacteria domain 0.91 "Deinococcus-Thermus" phylum 0.04 Deinococci class 0.04 Thermales order 0.04 Thermaceae family 0.04 Marinithermus genus 0.04
OTU_33 Root rootrank 1.0 Bacteria domain 0.88 "Proteobacteria" phylum 0.32 Deltaproteobacteria class 0.09 Myxococcales order 0.07 Cystobacterineae suborder 0.05 Myxococcaceae family 0.01 Pyxidicoccus genus 0.0
OTU_34 Root rootrank 1.0 Bacteria domain 0.93 "Actinobacteria" phylum 0.09 Actinobacteria class 0.08 Coriobacteridae subclass 0.04 Coriobacteriales order 0.04 "Coriobacterineae" suborder 0.04 Coriobacteriaceae family 0.04 Adlercreutzia genus 0.03
OTU_35 Root rootrank 1.0 Bacteria domain 0.87 "Aquificae" phylum 0.12 Aquificae class 0.12 Desulfurobacteriales order 0.12 Desulfurobacteriaceae family 0.12 Balnearium genus 0.07
OTU_36 - Root rootrank 1.0 Bacteria domain 0.87 "Bacteroidetes" phylum 0.18 Cytophagia class 0.15 Cytophagales order 0.15 Cytophagaceae family 0.1 Persicitalea genus 0.09
OTU_37 Root rootrank 1.0 Bacteria domain 0.99 "Planctomycetes" phylum 0.2 Planctomycetia class 0.2 Planctomycetales order 0.16 Planctomycetaceae family 0.16 Aquisphaera genus 0.07
OTU_38 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Staphylococcaceae family 0.99 Staphylococcus genus 0.99
OTU_39 - Root rootrank 1.0 Bacteria domain 0.92 "Proteobacteria" phylum 0.48 Betaproteobacteria class 0.17 Burkholderiales order 0.06 Comamonadaceae family 0.06 Tepidicella genus 0.06
OTU_40 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.98 Listeriaceae family 0.96 Listeria genus 0.96
OTU_41 - Root rootrank 1.0 Archaea domain 0.38 "Crenarchaeota" phylum 0.09 Thermoprotei class 0.09 Thermoproteales order 0.04 Thermoproteaceae family 0.04 Caldivirga genus 0.01
OTU_42 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 0.99 Bacilli class 0.99 Lactobacillales order 0.99 Lactobacillaceae family 0.98 Lactobacillus genus 0.96
OTU_43 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.98 Bacillaceae 2 family 0.79 Allobacillus genus 0.55
OTU_44 Root rootrank 1.0 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Bacteroidia" class 1.0 "Bacteroidales" order 1.0 "Porphyromonadaceae" family 0.98 Barnesiella genus 0.33
OTU_45 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.96 Deltaproteobacteria class 0.95 Bdellovibrionales order 0.95 Bdellovibrionaceae family 0.95 Vampirovibrio genus 0.95
OTU_46 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.89 Bacillus genus 0.89
OTU_47 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 0.79 Listeria genus 0.79
OTU_48 - Root rootrank 1.0 Archaea domain 0.12 Diapherotrites phylum 0.02 Candidatus Iainarchaeum genus 0.02
OTU_49 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.86 Bacillus genus 0.85
OTU_50 Root rootrank 1.0 Bacteria domain 0.77 "Bacteroidetes" phylum 0.15 Cytophagia class 0.04 Cytophagales order 0.04 Cytophagaceae family 0.04 Persicitalea genus 0.02
OTU_51 - Root rootrank 1.0 Bacteria domain 0.9 "Spirochaetes" phylum 0.06 Spirochaetia class 0.06 Spirochaetales order 0.06 Spirochaetales_incertae_sedis family 0.04 Exilispira genus 0.04
OTU_52 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.98 Enterococcaceae family 0.56 Enterococcus genus 0.31
OTU_53 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.78 Enterococcaceae family 0.6 Melissococcus genus 0.2
OTU_54 Root rootrank 1.0 Bacteria domain 0.93 "Bacteroidetes" phylum 0.26 "Bacteroidia" class 0.07 "Bacteroidales" order 0.07 "Bacteroidales"_incertae_sedis family 0.05 Phocaeicola genus 0.05
OTU_55 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.56 Gammaproteobacteria class 0.56 "Enterobacteriales" order 0.54 Enterobacteriaceae family 0.54 Cosenzaea genus 0.18
OTU_56 Root rootrank 1.0 Bacteria domain 0.91 Firmicutes phylum 0.27 Clostridia class 0.19 Clostridiales order 0.16 Peptococcaceae 2 family 0.04 Cryptanaerobacter genus 0.04
OTU_57 Root rootrank 1.0 Archaea domain 0.11 "Euryarchaeota" phylum 0.09 Thermoplasmata class 0.08 Methanomassiliicoccales order 0.08 Methanomassiliicoccaceae family 0.08 Methanomassiliicoccus genus 0.08
OTU_58 - Root rootrank 1.0 Bacteria domain 0.72 "Chloroflexi" phylum 0.12 Chloroflexia class 0.12 Kallotenuales order 0.12 Kallotenuaceae family 0.12 Kallotenue genus 0.12
OTU_59 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Sphingomonadales order 1.0 Sphingomonadaceae family 1.0 Sphingomonas genus 1.0
OTU_60 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_61 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.97 Staphylococcaceae family 0.96 Staphylococcus genus 0.95
OTU_62 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 0.59 Bacilli class 0.59 Bacillales order 0.52 Planococcaceae family 0.15 Solibacillus genus 0.14
OTU_63 Root rootrank 1.0 Bacteria domain 0.9 "Tenericutes" phylum 0.04 Mollicutes class 0.04 Anaeroplasmatales order 0.03 Anaeroplasmataceae family 0.03 Asteroleplasma genus 0.03
OTU_64 Root rootrank 1.0 Bacteria domain 0.71 "Deinococcus-Thermus" phylum 0.08 Deinococci class 0.08 Thermales order 0.07 Thermaceae family 0.07 Vulcanithermus genus 0.05
OTU_65 Root rootrank 1.0 Bacteria domain 1.0 "Fusobacteria" phylum 1.0 Fusobacteriia class 1.0 "Fusobacteriales" order 1.0 "Leptotrichiaceae" family 1.0 Sneathia genus 0.57
OTU_66 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.33 Carnobacteriaceae family 0.28 Isobaculum genus 0.11
OTU_67 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.85 Enterococcaceae family 0.85 Enterococcus genus 0.73
OTU_68 - Root rootrank 1.0 Bacteria domain 0.92 Firmicutes phylum 0.34 Clostridia class 0.24 Clostridiales order 0.21 Lachnospiraceae family 0.04 Howardella genus 0.03
OTU_69 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_70 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.99 Lactobacillaceae family 0.98 Lactobacillus genus 0.98
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);
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