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Amine GHOZLANE
shaman
Commits
ed1db183
Commit
ed1db183
authored
Aug 13, 2019
by
Amine GHOZLANE
Browse files
Add sample_metadata support from biomformat and example data
parent
b9931fa0
Changes
16
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.gitignore
View file @
ed1db183
...
...
@@ -3,9 +3,7 @@
*.RData
.Rproj.user
*.Rproj
*.json
www/masque/doing/*
www/masque/todo/*
www/masque/done/*
www/masque/error/*
www/masque.png
\ No newline at end of file
www/masque.png
Rfunctions/Data_Management.R
View file @
ed1db183
...
...
@@ -496,7 +496,7 @@ PercentAnnot <- function(counts,taxo)
}
## Get the counts and the ta
xo
tables from the BIOM format file.
## Get the counts
, the taxo
and the ta
rget
tables from the BIOM format file.
GetDataFromBIOM
<-
function
(
dataBIOM
)
{
taxo
=
NULL
...
...
@@ -515,14 +515,15 @@ GetDataFromBIOM <-function(dataBIOM)
counts
=
CheckCounts
$
counts
## Taxonomy table
tmp
=
observation_metadata
(
dataBIOM
)
if
(
!
is.null
(
tmp
))
obs
=
observation_metadata
(
dataBIOM
)
if
(
!
is.null
(
obs
))
{
if
(
is.data.frame
(
tmp
))
taxo
=
as.data.frame
(
tmp
)
if
(
!
is.data.frame
(
tmp
))
taxo
=
as.data.frame
(
t
(
sapply
(
observation_metadata
(
dataBIOM
),
FUN
=
function
(
x
){
x
[
1
:
7
]})))
if
(
is.data.frame
(
obs
))
taxo
=
as.data.frame
(
obs
)
if
(
!
is.data.frame
(
obs
))
taxo
=
as.data.frame
(
t
(
sapply
(
observation_metadata
(
dataBIOM
),
FUN
=
function
(
x
){
x
[
1
:
7
]})))
OTUnames
=
rownames
(
taxo
)
## Modif taxo table (remove p__,... and change the colnames)
taxo_biom
=
taxo
taxo
=
as.data.frame
(
sapply
(
taxo
,
gsub
,
pattern
=
"^.*__"
,
replacement
=
""
))
colnames
(
taxo
)
=
c
(
"Kingdom"
,
"Phylum"
,
"Class"
,
"Order"
,
"Family"
,
"Genus"
,
"Species"
)
rownames
(
taxo
)
=
OTUnames
...
...
@@ -531,19 +532,34 @@ GetDataFromBIOM <-function(dataBIOM)
taxo
[
taxo
==
"Unassigned"
]
=
NA
taxo
=
taxo
[
rowSums
(
is.na
(
taxo
))
!=
dim
(
taxo
)[
2
],
]
}
if
(
is.null
(
tmp
)
&&
!
is.null
(
counts
))
{
taxo
=
data.frame
(
rownames
(
counts
),
row.names
=
rownames
(
counts
));
names
(
taxo
)
=
NA
;
taxoCreated
=
TRUE
}
## Sample metadata
target
=
sample_metadata
(
dataBIOM
)
if
(
!
is.null
(
target
))
{
# Convert from list to dataframe
target
=
as.data.frame
(
target
)
target
$
SampleID
=
rownames
(
target
)
print
(
c
(
dim
(
target
)[
2
],
seq
(
1
,
dim
(
target
)[
2
]
-1
)))
target
=
subset
(
target
,
select
=
c
(
dim
(
target
)[
2
],
seq
(
1
,
dim
(
target
)[
2
]
-1
)))
}
print
(
target
)
if
(
is.null
(
obs
)
&&
!
is.null
(
counts
))
{
taxo
=
data.frame
(
rownames
(
counts
),
row.names
=
rownames
(
counts
));
names
(
taxo
)
=
NA
;
taxoCreated
=
TRUE
}
CheckTaxo
=
CheckTaxoTable
(
taxo
,
counts
,
taxoCreated
)
#input the target file
#CheckTargetModel(,meta,)
## Pourcentage of annotation
tmp
=
PercentAnnot
(
counts
,
taxo
)
perca
=
PercentAnnot
(
counts
,
taxo
)
return
(
list
(
counts
=
counts
,
taxo
=
taxo
,
CheckCounts
=
CheckCounts
,
CheckTaxo
=
CheckTaxo
,
Percent
=
tmp
$
Percent
,
CheckPercent
=
tmp
$
Error
))
return
(
list
(
counts
=
counts
,
taxo
=
taxo
,
taxo_biom
=
taxo_biom
,
target
=
target
,
CheckCounts
=
CheckCounts
,
CheckTaxo
=
CheckTaxo
,
Percent
=
perca
$
Percent
,
CheckPercent
=
perca
$
Error
))
}
## Check the data
GetDataFromCT
<-
function
(
dataC
,
dataT
,
MGSTable
)
{
l
=
c
(
"k__"
,
"p__"
,
"c__"
,
"o__"
,
"f__"
,
"g__"
,
"s__"
)
## Counts table
counts
=
dataC
...
...
@@ -554,11 +570,26 @@ GetDataFromCT <-function(dataC,dataT, MGSTable)
## Taxonomy table
taxo
=
as.data.frame
(
dataT
)
CheckTaxo
=
CheckTaxoTable
(
taxo
,
counts
,
MGSTable
)
# Biom taxonomy must have seven levels
taxo_temp
=
as.matrix
(
taxo
)
if
(
dim
(
taxo_temp
)[
2
]
<
7
){
taxo_temp
=
cbind
(
taxo_temp
,
matrix
(
NA
,
dim
(
taxo_temp
)[
1
],
7
-
dim
(
taxo_temp
)[
2
]))
}
# All OTU must be referenced
if
(
dim
(
taxo_temp
)[
1
]
!=
dim
(
counts
)[
1
]){
missing_elements
=
rownames
(
counts
)[
!
rownames
(
counts
)
%in%
rownames
(
taxo_temp
)]
mat_missing
=
matrix
(
NA
,
length
(
missing_elements
),
dim
(
taxo_temp
)[
2
])
rownames
(
mat_missing
)
=
missing_elements
taxo_temp
=
rbind
(
taxo_temp
,
mat_missing
)
}
taxo_biom
=
t
(
sapply
(
as.data.frame
(
t
(
taxo_temp
)),
FUN
=
function
(
x
){
paste
(
l
,
na.omit
(
x
),
sep
=
""
)}))
## Pourcentage of annotation
tmp
=
PercentAnnot
(
counts
,
taxo
)
return
(
list
(
counts
=
counts
,
taxo
=
taxo
,
CheckCounts
=
CheckCounts
,
CheckTaxo
=
CheckTaxo
,
Percent
=
tmp
$
Percent
,
CheckPercent
=
tmp
$
Error
))
return
(
list
(
counts
=
counts
,
taxo
=
taxo
,
taxo_biom
=
taxo_biom
,
CheckCounts
=
CheckCounts
,
CheckTaxo
=
CheckTaxo
,
Percent
=
tmp
$
Percent
,
CheckPercent
=
tmp
$
Error
))
}
...
...
server.R
View file @
ed1db183
...
...
@@ -16,7 +16,6 @@ shinyServer(function(input, output,session) {
file.create
(
namesfile
,
showWarnings
=
FALSE
)
target
=
NULL
## JSON name for masque
curdir
=
getwd
()
json_name
=
tempfile
(
pattern
=
"file"
,
tmpdir
=
paste
(
curdir
,
"www"
,
"masque"
,
"todo"
,
sep
=
.Platform
$
file.sep
),
fileext
=
".json"
)
...
...
@@ -257,6 +256,7 @@ shinyServer(function(input, output,session) {
Taxo
=
NULL
Counts
=
NULL
inputData
=
NULL
target
=
NULL
if
(
input
$
FileFormat
==
"fileCounts"
)
{
...
...
@@ -267,7 +267,7 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
Counts
)
&&
!
is.null
(
Taxo
))
{
tmp
=
GetDataFromCT
(
Counts
,
Taxo
,
ifelse
(
input
$
TypeTable
==
"MGS"
&&
input
$
FileFormat
!=
"fileBiom"
,
TRUE
,
FALSE
))
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
)
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
,
taxo_biom
=
tmp
$
taxo_biom
)
## Remove row with only O
# data[["counts"]] = data[["counts"]][rowSums(data[["counts"]])>1,]
...
...
@@ -282,12 +282,13 @@ shinyServer(function(input, output,session) {
if
(
!
is.null
(
tmpBIOM
))
{
tmp
=
GetDataFromBIOM
(
tmpBIOM
)
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
)
data
=
list
(
counts
=
tmp
$
counts
,
taxo
=
tmp
$
taxo
,
target
=
tmp
$
target
,
taxo_biom
=
tmp
$
taxo_biom
)
## Remove row with only O
# data[["counts"]] = data[["counts"]][rowSums(data[["counts"]])>1,]
check
=
list
(
CheckCounts
=
tmp
$
CheckCounts
,
CheckTaxo
=
tmp
$
CheckTaxo
,
CheckPercent
=
tmp
$
CheckPercent
)
percent
=
tmp
$
Percent
#if(!is.null(data$target)) values$TargetWorking = data$target
}
}
...
...
@@ -720,12 +721,39 @@ shinyServer(function(input, output,session) {
## TARGET FILE
##
#####################################################
observe
({
counts
=
dataInput
()
$
data
$
counts
data
=
dataInput
()
$
data
$
target
if
(
!
is.null
(
data
)
&&
!
is.null
(
counts
))
{
names
=
colnames
(
data
)
## Keep only the row which are in the count table
ind
=
which
(
rownames
(
data
)
%in%
colnames
(
counts
))
data
=
as.data.frame
(
data
[
ind
,])
colnames
(
data
)
=
names
## Replace "-" by "."
if
(
ncol
(
data
)
>
1
&&
nrow
(
data
)
>
1
){
ind_num
=
which
(
sapply
(
as.data.frame
(
data
[,
-1
]),
is.numeric
))
+
1
if
(
length
(
ind_num
)
>
0
){
data_tmp
=
cbind
(
as.data.frame
(
apply
(
as.data.frame
(
data
[,
-
ind_num
]),
2
,
gsub
,
pattern
=
"-"
,
replacement
=
"."
)),
data
[,
ind_num
])
#data_tmp =cbind( as.data.frame(as.data.frame(data[,-ind_num])),data[,ind_num])
colnames
(
data_tmp
)
=
c
(
colnames
(
data
)[
-
ind_num
],
colnames
(
data
)[
ind_num
])
data
=
data_tmp
}
if
(
length
(
ind_num
)
==
0
){
data
=
as.data.frame
(
apply
(
data
,
2
,
gsub
,
pattern
=
"-"
,
replacement
=
"."
))}
}
values
$
TargetWorking
=
data
values
$
labeled
=
length
(
ind
)
/
length
(
colnames
(
counts
))
*
100.0
}
})
## Load target file
observe
({
inFile
<-
input
$
fileTarget
#values$TargetWorking = NULL
counts
=
dataInput
()
$
data
$
counts
labeled
=
0
data
=
NULL
...
...
@@ -760,7 +788,6 @@ shinyServer(function(input, output,session) {
}
if
(
length
(
ind_num
)
==
0
){
data
=
as.data.frame
(
apply
(
data
,
2
,
gsub
,
pattern
=
"-"
,
replacement
=
"."
))}
}
values
$
TargetWorking
=
as.data.frame
(
data
)
# ind_sel = Target_selection()
# if(length(ind))
...
...
@@ -768,8 +795,8 @@ shinyServer(function(input, output,session) {
#ord = order(rownames(data))
#data = data[ord,]
### A SUPPRIMER
#rownames(data) <- colnames(counts)
### A SU
q
PPRIMER
#rownam
Q
es(data) <- colnames(counts)
# Percent annotated
# print(ind)
...
...
@@ -1370,9 +1397,21 @@ shinyServer(function(input, output,session) {
removeCssClass
(
class
=
'pwdGREEN'
,
selector
=
'#password'
)
}
})
# Run demo
observeEvent
(
input
$
DemoDataset
,
{
if
(
input
$
DemoDataset
!=
"..."
){
values
$
masque_key
=
input
$
DemoDataset
updateSelectInput
(
session
,
"FileFormat"
,
""
,
selected
=
"fileBiom"
)
reset
(
"fileBiom"
)
reset
(
"fileTree"
)
values
$
biom_masque
=
paste
(
values
$
curdir
,
"www"
,
"masque"
,
"done"
,
paste
(
"file"
,
values
$
masque_key
,
sep
=
""
),
paste
(
"shaman_silva.biom"
,
sep
=
""
),
sep
=
.Platform
$
file.sep
)
values
$
tree_masque
=
paste
(
values
$
curdir
,
"www"
,
"masque"
,
"done"
,
paste
(
"file"
,
values
$
masque_key
,
sep
=
""
),
paste
(
"shaman_silva_tree.nhx"
,
sep
=
""
),
sep
=
.Platform
$
file.sep
)
sendSweetAlert
(
messageId
=
"DemoDataset"
,
title
=
"Success"
,
text
=
"Data of XXX were successfully loaded. You can go to statistical analysis section."
,
type
=
"success"
,
html
=
TRUE
)
}
})
## the same from home
observeEvent
(
input
$
Check_project_home
,{
observeEvent
(
input
$
Check_project_home
,
{
values
$
masque_key
=
input
$
password_home
PS
=
Project_status
(
values
$
masque_key
,
values
$
curdir
)
...
...
@@ -1400,6 +1439,14 @@ shinyServer(function(input, output,session) {
})
# observeEvent(input$DemoDataset,{
# if(input$DemoDataset != "...")
# values$masque_key = input$DemoDataset
#
# PS = Project_status(values$masque_key,values$curdir)
# })
#eventReactive(input$refresh, {
# shinyjs::js$refresh()
#hideElement("gaugeMasque_progress")
...
...
@@ -2022,22 +2069,40 @@ shinyServer(function(input, output,session) {
## Box for merged counts
output
$
BoxCountsMerge
<-
renderUI
({
input
$
RunDESeq
#counts = isolate(dataMergeCounts()$counts)
#
input$RunDESeq
#
#counts = isolate(dataMergeCounts()$counts)
counts
=
isolate
(
dataMergeCounts
()
$
CT_Norm
)
taxo
=
input
$
TaxoSelect
#
# if(!is.null(counts) && taxo != "...")
# {
resDiff
=
ResDiffAnal
()
int
=
input
$
Interaction2
if
(
!
is.null
(
counts
)
&&
taxo
!=
"..."
)
{
if
(
!
is.null
(
resDiff
)){
box
(
title
=
paste
(
"Count table ("
,
taxo
,
")"
,
sep
=
""
),
width
=
NULL
,
status
=
"primary"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
collapsed
=
TRUE
,
DT
::
dataTableOutput
(
"CountsMerge"
),
downloadButton
(
'ExportCounts'
,
'Export normali
s
ed counts'
),
downloadButton
(
'ExportCounts'
,
'Export normali
z
ed counts'
),
downloadButton
(
'ExportRelative'
,
'Export relative abundance'
)
)
}
})
output
$
ButtonBiom
<-
renderUI
({
resDiff
=
ResDiffAnal
()
int
=
input
$
Interaction2
if
(
!
is.null
(
resDiff
))
downloadButton
(
'ExportBiom'
,
'Export BIOM'
)
})
output
$
ExportBiom
<-
downloadHandler
(
filename
=
function
()
{
'SHAMAN_data.biom'
},
#write_biom doesn't handle properly the sample metadata
content
=
function
(
file
){
write_biom
(
make_biom
(
dataMergeCounts
()
$
CT_noNorm
,
sample_metadata
=
values
$
TargetWorking
[,
-1
],
observation_metadata
=
dataInput
()
$
data
$
taxo_biom
),
file
)}
)
## Export in .csv
output
$
ExportCounts
<-
downloadHandler
(
filename
=
function
()
{
'NormCounts.csv'
},
...
...
@@ -2048,7 +2113,8 @@ shinyServer(function(input, output,session) {
## Export in .csv
output
$
ExportRelative
<-
downloadHandler
(
filename
=
function
()
{
'RelativeAb.csv'
},
content
=
function
(
file
){
write.csv
(
sweep
(
round
(
counts
(
ResDiffAnal
()
$
dds
,
normalized
=
TRUE
)),
2
,
colSums
(
round
(
counts
(
ResDiffAnal
()
$
dds
,
normalized
=
TRUE
))),
`/`
),
file
)}
content
=
function
(
file
){
write.csv
(
sweep
(
round
(
counts
(
ResDiffAnal
()
$
dds
,
normalized
=
TRUE
)),
2
,
colSums
(
round
(
counts
(
ResDiffAnal
()
$
dds
,
normalized
=
TRUE
))),
`/`
),
file
)}
)
## Export size factors
...
...
@@ -4299,13 +4365,10 @@ shinyServer(function(input, output,session) {
observe
({
taxo
=
input
$
TaxoSelect
target
=
values
$
TargetWorking
if
(
is.null
(
target
)
||
is.null
(
taxo
))
shinyjs
::
disable
(
"AddFilter"
)
else
if
(
is.null
(
target
)
||
taxo
==
"..."
)
shinyjs
::
disable
(
"AddFilter"
)
else
shinyjs
::
enable
(
"AddFilter"
)
if
(
is.null
(
target
)
||
taxo
==
"..."
)
{
shinyjs
::
disable
(
"AddFilter"
)
}
else
{
shinyjs
::
enable
(
"AddFilter"
)
}
})
###########
...
...
ui.R
View file @
ed1db183
...
...
@@ -59,7 +59,7 @@ function(request) {
tabPanel
(
"Authors"
,
h3
(
"The main contributors to SHAMAN:"
),
p
(
a
(
"Stevenn Volant"
,
href
=
"mailto:stevenn.volant@pasteur.fr"
),
"(Initiator, coding, testing, documentation, evaluation)"
),
p
(
a
(
"Amine Ghozlane"
,
href
=
"mailto:amine.ghozlane@pasteur.fr"
),
"(Coding, testing, documentation, evaluation, packaging)"
),
p
(
"Perrine Woringer"
,
"(Coding, testing,
D
ocumentation)"
),
p
(
"Perrine Woringer"
,
"(Coding, testing,
d
ocumentation
, feature suggestions
)"
),
p
(
"Pierre Lechat"
,
"(Coding, testing, feature suggestions)"
),
h3
(
"Acknowledgements"
),
p
(
"Thanks to the following people for patches and other suggestions for improvements:"
),
...
...
@@ -518,7 +518,9 @@ function(request) {
# selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Saved project"="fileRData"),selected="fileCounts"),
selectInput
(
"FileFormat"
,
""
,
c
(
"Count table & taxonomy (*.csv or *.tsv)"
=
"fileCounts"
,
"BIOM file"
=
"fileBiom"
,
"Project number"
=
"projnum"
),
selected
=
"fileCounts"
),
conditionalPanel
(
condition
=
"input.FileFormat=='fileCounts'"
,
checkboxInput
(
"NoTaxoFile"
,
"No taxonomy table"
,
value
=
FALSE
)
checkboxInput
(
"NoTaxoFile"
,
"No taxonomy table"
,
value
=
FALSE
),
selectInput
(
"DemoDataset"
,
h6
(
strong
(
'Or select a dataset'
)),
c
(
"..."
=
"..."
,
"ZymoBIOMICS mock 16S"
=
"30a47fca2dc3"
),
selected
=
"..."
),
receiveSweetAlert
(
messageId
=
"DemoDataset"
)
),
conditionalPanel
(
condition
=
"input.FileFormat=='projnum'"
,
inlineCSS
(
list
(
.pwdGREEN
=
"background-color: #DDF0B3"
,
.pwdRED
=
"background-color: #F0B2AD"
)),
...
...
@@ -619,6 +621,8 @@ function(request) {
column
(
width
=
6
,
uiOutput
(
"SelectInteraction2"
))
),
fluidRow
(
column
(
width
=
6
,
uiOutput
(
'ButtonBiom'
)),
#column(width=6,downloadButton('ExportBiom', 'Export BIOM')),
column
(
width
=
6
,
uiOutput
(
"RunButton"
))
)
),
...
...
www/masque/done/file30a47fca2dc3.json
0 → 100644
View file @
ed1db183
{
"contaminant"
:
"/tmp/Rtmpimkesv/file873bc712cf0_contaminant.fasta"
,
"data_history_name"
:
"data_shaman_37694_0"
,
"paired"
:
true
,
"host"
:
""
,
"type"
:
"16S"
,
"pattern_R1"
:
"_R1"
,
"result_history_name"
:
"shaman_37694_0"
,
"path_R2"
:
"/tmp/Rtmpimkesv/Masque_files_R2"
,
"mail"
:
"amine.ghozlane@pasteur.fr"
,
"name"
:
"file873bc712cf0"
,
"path_R1"
:
"/tmp/Rtmpimkesv/Masque_files_R1"
}
\ No newline at end of file
www/masque/done/file30a47fca2dc3/shaman_greengenes.biom
0 → 100644
View file @
ed1db183
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:18:38","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_11","metadata":["k__Bacteria","p__Cyanobacteria","c__4C0d-2","o__MLE1-12","f__Bacteria","g__Cyanobacteria","s__4C0d-2"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Betaproteobacteria","o__Burkholderiales","f__Comamonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_17","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_18","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_19","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_2","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_20","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_21","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_22","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_23","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_24","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_25","metadata":["k__Bacteria","p__Bacteroidetes","c__Bacteroidia","o__Bacteroidales","f__S24-7","g__Bacteria","s__Bacteroidetes"]},{"id":"OTU_26","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_27","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_28","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_29","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_3","metadata":["k__Bacteria","p__Actinobacteria","c__Actinobacteria","o__Actinomycetales","f__Propionibacteriaceae","g__Propionibacterium","s__acnes"]},{"id":"OTU_30","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_31","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_32","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_33","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_34","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_35","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_36","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_37","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_38","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_39","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_4","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_40","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_41","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_42","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_43","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_44","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_45","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_46","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_47","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_48","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_49","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_5","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_50","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_51","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_52","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_53","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_54","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_55","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_56","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_57","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_58","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_59","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_6","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_60","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_61","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_62","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_63","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_7","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_8","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_9","metadata":["k__","p__","c__","o__","f__","g__","s__"]}],"columns":[{"id":"1ng.25cycles.1_S38_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.2_S39_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.3_S40_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.30cycles.1_S50_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.2_S51_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.3_S52_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"20ng.20cycles.1_S14_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.2_S15_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.3_S16_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.25cycles.1_S2_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.2_S3_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.3_S4_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.1_S26_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.2_S27_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.3_S28_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.1_S62_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.2_S63_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.3_S64_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.30cycles.1_S74_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.2_S75_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.3_S76_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}}],"data":[[17452,27133,22628,34080,44295,26503,37448,44573,39161,39050,32932,40607,25728,29573,31779,37086,38992,27499,43560,25485,6836],[13,0,12,22,3,5,18,18,11,24,1,12,37,0,22,22,4,16,43,8,3],[2,1,3,28,1,2,10,11,1,11,8,8,16,6,20,5,1,9,10,13,3],[11,29,14,55,74,41,35,48,20,45,75,62,49,65,41,18,43,19,52,52,4],[20,40,34,76,116,38,35,70,51,70,113,79,32,74,72,43,64,24,77,48,5],[0,6,3,8,9,8,0,0,0,0,0,0,0,3,0,12,18,5,13,6,0],[23,62,30,79,149,57,39,72,59,86,106,100,62,47,51,51,67,34,63,90,10],[0,2,0,4,4,0,6,3,2,5,3,1,1,2,6,1,0,2,9,5,0],[5,0,0,4,4,0,0,1,2,4,0,7,5,1,1,0,0,1,5,0,0],[3,1,0,14,4,0,4,4,9,2,6,4,6,5,3,1,0,1,8,5,2],[1,4,3,10,4,2,0,0,1,0,0,0,0,2,1,14,6,1,15,5,3],[15860,23646,22078,29667,43537,24072,36479,47320,38806,32012,25103,30496,26135,34793,32500,38523,42830,30774,39737,28634,4774],[0,0,0,0,5,1,1,0,2,1,0,5,4,0,0,0,1,1,7,0,0],[13,23,11,54,78,31,13,60,44,66,66,57,22,51,53,22,33,17,61,37,5],[10,17,12,34,56,32,14,23,18,55,38,49,20,36,16,13,32,6,53,21,7],[0,1,0,4,1,1,0,0,0,2,1,1,7,0,1,3,3,0,2,4,0],[0,0,0,3,0,2,0,3,7,2,0,0,4,0,1,3,0,0,2,2,0],[18,42,20,68,88,57,37,48,35,86,90,68,52,80,65,32,59,20,80,61,11],[1,1,1,7,1,0,0,0,1,0,0,0,5,1,0,2,2,0,3,1,0],[1,0,1,1,0,0,0,3,1,1,1,0,0,3,2,0,0,2,0,0,0],[0,0,0,2,0,1,0,0,0,0,0,1,0,2,0,1,0,0,1,2,0],[1,0,0,0,0,1,4,1,2,3,0,1,1,4,0,1,2,1,7,6,1],[13125,22105,17509,23529,36814,19721,30956,43056,33082,25061,23471,26121,20873,27980,28509,32630,38907,27115,30649,23025,3775],[2,3,0,2,0,2,1,2,0,1,0,1,0,0,0,0,0,2,2,0,0],[1,0,0,2,2,0,0,0,0,2,2,1,0,1,1,0,0,1,4,0,0],[31,67,36,143,204,64,86,131,66,124,135,114,86,116,117,74,109,60,189,86,20],[111,221,114,414,591,245,197,336,241,391,448,394,231,379,317,186,311,109,506,319,61],[0,1,0,0,1,0,0,2,0,0,3,0,2,2,1,2,2,0,2,1,0],[0,0,0,0,3,0,4,1,0,2,0,2,0,0,0,0,0,0,2,0,0],[0,0,0,0,1,0,0,0,0,0,0,0,2,2,0,0,0,0,4,2,0],[1,3,2,4,7,1,5,0,0,0,2,0,0,1,5,1,3,1,2,4,0],[225,379,195,805,1014,423,387,669,422,858,826,711,406,628,505,341,511,249,1032,668,30],[5,2,1,1,4,3,0,0,0,4,1,0,2,3,4,0,0,0,5,0,0],[13337,23359,16051,28762,41768,20948,35150,39582,31692,31582,26212,25297,25494,32339,34775,39042,38318,25859,39136,26583,2790],[0,0,5,2,0,0,0,2,2,1,0,2,0,0,0,2,0,0,3,0,0],[0,0,0,0,1,0,0,3,1,0,2,0,0,0,0,0,0,1,3,1,0],[2,4,1,16,15,8,2,4,5,33,28,9,9,5,8,4,1,0,20,15,3],[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,2,3,0,10,0],[195,379,163,976,1055,534,504,662,366,1009,867,564,595,730,708,421,503,222,1225,583,85],[76,149,84,320,410,129,150,252,132,329,309,278,162,237,190,101,194,94,409,240,22],[0,0,0,2,0,0,0,0,0,0,0,1,3,0,1,0,0,1,0,0,0],[0,0,2,0,0,1,0,0,0,1,0,2,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,2,0,0,0,0,0],[0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,6,1,1,5,2,0],[11531,20057,16044,23534,35804,15246,26747,35766,29197,26834,24773,29176,19939,27576,27496,27523,33651,24155,31504,22764,1540],[0,0,0,0,0,0,0,0,0,5,0,0,0,0,1,1,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0],[0,0,0,2,0,0,0,0,0,3,0,0,0,0,0,0,0,0,3,0,0],[0,0,1,2,0,0,3,3,3,1,1,1,5,2,0,1,0,0,6,3,0],[36,50,24,100,95,47,64,74,46,91,89,111,56,84,59,37,45,20,140,83,3],[249,450,266,1061,1311,492,477,712,443,1093,933,930,542,916,663,398,548,274,1285,737,49],[1,0,0,2,0,0,0,0,2,0,0,2,1,1,1,1,2,2,2,3,0],[41,59,27,171,185,84,54,91,74,173,163,170,95,90,127,30,76,61,200,139,10],[5,5,6,17,27,17,11,5,12,25,28,24,15,11,25,3,6,6,45,18,1],[1,0,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0,0,0,0],[8183,13707,10964,16276,24625,12822,18729,23977,19123,17982,17070,19830,13793,18802,17884,18929,23174,15187,21971,15719,2336],[17,44,12,101,137,71,36,100,59,94,86,118,59,90,71,46,51,32,122,72,17],[1,1,0,9,6,10,7,5,3,5,6,8,1,8,1,1,5,1,9,4,2],[3,3,2,42,29,14,1,9,1,37,24,16,3,15,7,5,1,1,25,12,2],[0,2,0,2,0,0,0,0,0,0,0,3,0,0,1,0,0,0,6,0,0],[6506,11883,8080,11966,19193,9309,14386,19327,15146,13448,12560,13118,9135,12995,13890,15038,18146,11681,15168,11666,2165],[5082,9047,7033,10887,16871,6722,12362,18325,14321,11921,11802,13621,9812,13294,13394,12133,15601,9962,15972,11023,651],[7,5,17,39,8,6,29,26,19,32,1,22,47,6,51,17,0,22,58,17,3]]}
\ No newline at end of file
www/masque/done/file30a47fca2dc3/shaman_greengenes_annotation.tsv
0 → 100644
View file @
ed1db183
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_15 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_58 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_36 Bacteria Cyanobacteria 4C0d-2 MLE1-12
OTU_4 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_23 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_14 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae
OTU_12 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_1 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_26 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_33 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_62 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_49 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae
OTU_44 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_60 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_13 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_55 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_21 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_43 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7
OTU_25 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_6 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_41 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_2 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_19 Bacteria Actinobacteria Actinobacteria Actinomycetales Propionibacteriaceae Propionibacterium acnes
OTU_37 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_22 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_42 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_57 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_45 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_3 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_38 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_34 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_39 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_61 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_5 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_31 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_32 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_7 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_54 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
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#OTU ID 1ng-25cycles-1_S38_L001_001 1ng-25cycles-2_S39_L001_001 1ng-25cycles-3_S40_L001_001 1ng-30cycles-1_S50_L001_001 1ng-30cycles-2_S51_L001_001 1ng-30cycles-3_S52_L001_001 20ng-20cycles-1_S14_L001_001 20ng-20cycles-2_S15_L001_001 20ng-20cycles-3_S16_L001_001 20ng-25cycles-1_S2_L001_001 20ng-25cycles-2_S3_L001_001 20ng-25cycles-3_S4_L001_001 5ng-25cycles-1_S26_L001_001 5ng-25cycles-2_S27_L001_001 5ng-25cycles-3_S28_L001_001 zero5ng-25cycles-1_S62_L001_001 zero5ng-25cycles-2_S63_L001_001 zero5ng-25cycles-3_S64_L001_001 zero5ng-30cycles-1_S74_L001_001 zero5ng-30cycles-2_S75_L001_001 zero5ng-30cycles-3_S76_L001_001
OTU_1 17452 27133 22628 34080 44295 26503 37448 44573 39161 39050 32932 40607 25728 29573 31779 37086 38992 27499 43560 25485 6836
OTU_10 13 0 12 22 3 5 18 18 11 24 1 12 37 0 22 22 4 16 43 8 3
OTU_11 2 1 3 28 1 2 10 11 1 11 8 8 16 6 20 5 1 9 10 13 3
OTU_12 11 29 14 55 74 41 35 48 20 45 75 62 49 65 41 18 43 19 52 52 4
OTU_13 20 40 34 76 116 38 35 70 51 70 113 79 32 74 72 43 64 24 77 48 5
OTU_14 0 6 3 8 9 8 0 0 0 0 0 0 0 3 0 12 18 5 13 6 0
OTU_15 23 62 30 79 149 57 39 72 59 86 106 100 62 47 51 51 67 34 63 90 10
OTU_16 0 2 0 4 4 0 6 3 2 5 3 1 1 2 6 1 0 2 9 5 0
OTU_17 5 0 0 4 4 0 0 1 2 4 0 7 5 1 1 0 0 1 5 0 0
OTU_18 3 1 0 14 4 0 4 4 9 2 6 4 6 5 3 1 0 1 8 5 2
OTU_19 1 4 3 10 4 2 0 0 1 0 0 0 0 2 1 14 6 1 15 5 3
OTU_2 15860 23646 22078 29667 43537 24072 36479 47320 38806 32012 25103 30496 26135 34793 32500 38523 42830 30774 39737 28634 4774
OTU_20 0 0 0 0 5 1 1 0 2 1 0 5 4 0 0 0 1 1 7 0 0
OTU_21 13 23 11 54 78 31 13 60 44 66 66 57 22 51 53 22 33 17 61 37 5
OTU_22 10 17 12 34 56 32 14 23 18 55 38 49 20 36 16 13 32 6 53 21 7
OTU_23 0 1 0 4 1 1 0 0 0 2 1 1 7 0 1 3 3 0 2 4 0
OTU_24 0 0 0 3 0 2 0 3 7 2 0 0 4 0 1 3 0 0 2 2 0
OTU_25 18 42 20 68 88 57 37 48 35 86 90 68 52 80 65 32 59 20 80 61 11
OTU_26 1 1 1 7 1 0 0 0 1 0 0 0 5 1 0 2 2 0 3 1 0
OTU_27 1 0 1 1 0 0 0 3 1 1 1 0 0 3 2 0 0 2 0 0 0
OTU_28 0 0 0 2 0 1 0 0 0 0 0 1 0 2 0 1 0 0 1 2 0
OTU_29 1 0 0 0 0 1 4 1 2 3 0 1 1 4 0 1 2 1 7 6 1
OTU_3 13125 22105 17509 23529 36814 19721 30956 43056 33082 25061 23471 26121 20873 27980 28509 32630 38907 27115 30649 23025 3775
OTU_30 2 3 0 2 0 2 1 2 0 1 0 1 0 0 0 0 0 2 2 0 0
OTU_31 1 0 0 2 2 0 0 0 0 2 2 1 0 1 1 0 0 1 4 0 0
OTU_32 31 67 36 143 204 64 86 131 66 124 135 114 86 116 117 74 109 60 189 86 20
OTU_33 111 221 114 414 591 245 197 336 241 391 448 394 231 379 317 186 311 109 506 319 61
OTU_34 0 1 0 0 1 0 0 2 0 0 3 0 2 2 1 2 2 0 2 1 0
OTU_35 0 0 0 0 3 0 4 1 0 2 0 2 0 0 0 0 0 0 2 0 0
OTU_36 0 0 0 0 1 0 0 0 0 0 0 0 2 2 0 0 0 0 4 2 0
OTU_37 1 3 2 4 7 1 5 0 0 0 2 0 0 1 5 1 3 1 2 4 0
OTU_38 225 379 195 805 1014 423 387 669 422 858 826 711 406 628 505 341 511 249 1032 668 30
OTU_39 5 2 1 1 4 3 0 0 0 4 1 0 2 3 4 0 0 0 5 0 0
OTU_4 13337 23359 16051 28762 41768 20948 35150 39582 31692 31582 26212 25297 25494 32339 34775 39042 38318 25859 39136 26583 2790
OTU_40 0 0 5 2 0 0 0 2 2 1 0 2 0 0 0 2 0 0 3 0 0
OTU_41 0 0 0 0 1 0 0 3 1 0 2 0 0 0 0 0 0 1 3 1 0
OTU_42 2 4 1 16 15 8 2 4 5 33 28 9 9 5 8 4 1 0 20 15 3
OTU_43 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 10 0
OTU_44 195 379 163 976 1055 534 504 662 366 1009 867 564 595 730 708 421 503 222 1225 583 85
OTU_45 76 149 84 320 410 129 150 252 132 329 309 278 162 237 190 101 194 94 409 240 22
OTU_46 0 0 0 2 0 0 0 0 0 0 0 1 3 0 1 0 0 1 0 0 0
OTU_47 0 0 2 0 0 1 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0
OTU_48 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2 0 0 0 0 0
OTU_49 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 6 1 1 5 2 0
OTU_5 11531 20057 16044 23534 35804 15246 26747 35766 29197 26834 24773 29176 19939 27576 27496 27523 33651 24155 31504 22764 1540
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0
OTU_52 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 0 0
OTU_53 0 0 1 2 0 0 3 3 3 1 1 1 5 2 0 1 0 0 6 3 0
OTU_54 36 50 24 100 95 47 64 74 46 91 89 111 56 84 59 37 45 20 140 83 3
OTU_55 249 450 266 1061 1311 492 477 712 443 1093 933 930 542 916 663 398 548 274 1285 737 49
OTU_56 1 0 0 2 0 0 0 0 2 0 0 2 1 1 1 1 2 2 2 3 0
OTU_57 41 59 27 171 185 84 54 91 74 173 163 170 95 90 127 30 76 61 200 139 10
OTU_58 5 5 6 17 27 17 11 5 12 25 28 24 15 11 25 3 6 6 45 18 1
OTU_59 1 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 0 0 0
OTU_6 8183 13707 10964 16276 24625 12822 18729 23977 19123 17982 17070 19830 13793 18802 17884 18929 23174 15187 21971 15719 2336
OTU_60 17 44 12 101 137 71 36 100 59 94 86 118 59 90 71 46 51 32 122 72 17
OTU_61 1 1 0 9 6 10 7 5 3 5 6 8 1 8 1 1 5 1 9 4 2
OTU_62 3 3 2 42 29 14 1 9 1 37 24 16 3 15 7 5 1 1 25 12 2
OTU_63 0 2 0 2 0 0 0 0 0 0 0 3 0 0 1 0 0 0 6 0 0
OTU_7 6506 11883 8080 11966 19193 9309 14386 19327 15146 13448 12560 13118 9135 12995 13890 15038 18146 11681 15168 11666 2165
OTU_8 5082 9047 7033 10887 16871 6722 12362 18325 14321 11921 11802 13621 9812 13294 13394 12133 15601 9962 15972 11023 651
OTU_9 7 5 17 39 8 6 29 26 19 32 1 22 47 6 51 17 0 22 58 17 3
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Type Count Mean_length Median_length
Amplicon 4248638 428 427
Dereplication 1629789 428 427
Singleton_removed 40537 429 427
Chimera_removed 34496 429 427
OTU 63 354 427
silva_annotation 39
greengenes_annotation 39
rdp_annotation 62
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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-1_S26_L001_001 216807 300 301 216807 300 300 403438 196888 206550 27842 17587 10255 192017 265 277 192017 227 231 167270 192017 60409 1507 1277 5 153559 79.97
20ng-25cycles-1_S2_L001_001 302678 300 301 302678 300 300 560043 274679 285364 42410 25097 17313 265513 265 277 265513 224 229 228922 265513 90528 2208 1749 5 202669 76.33
1ng-30cycles-1_S50_L001_001 275152 300 301 275152 300 300 509447 250179 259268 37693 21809 15884 242096 265 277 242096 222 227 209033 242096 84557 1998 1542 7 183410 75.76
zero5ng-25cycles-1_S62_L001_001 308283 300 301 308283 300 300 569407 277786 291621 43427 26767 16660 270219 265 277 270219 225 230 233528 270219 82353 2133 1951 2 222829 82.46
1ng-25cycles-3_S40_L001_001 172137 300 301 172137 300 300 315854 154559 161295 26482 15642 10840 149233 265 277 149233 223 227 128265 149233 48587 1285 1172 1 121491 81.41
5ng-25cycles-3_S28_L001_001 285903 300 301 285903 300 300 531229 257695 273534 37412 25043 12369 252430 264 277 252430 229 234 220357 252430 77958 1986 1662 4 203446 80.6
zero5ng-25cycles-2_S63_L001_001 352123 300 301 352123 300 300 648535 318719 329816 50482 28176 22306 308459 267 277 308459 221 226 266924 308459 98469 2510 2256 2 252325 81.8
zero5ng-25cycles-3_S64_L001_001 236495 300 301 236495 300 300 437038 212481 224557 33097 21161 11936 207488 265 277 207488 227 232 180797 207488 62110 1659 1557 2 173561 83.65
zero5ng-30cycles-1_S74_L001_001 359368 300 301 359368 300 300 665454 326768 338686 49132 28451 20681 316575 266 277 316575 223 227 274564 316575 105773 2526 1974 7 243522 76.92
1ng-25cycles-2_S39_L001_001 225513 300 301 225513 300 300 410838 203514 207324 37100 18912 18188 193922 267 277 193922 218 217 165528 193922 67393 1678 1445 2 152993 78.89
20ng-20cycles-1_S14_L001_001 297586 300 301 297586 300 300 550934 268644 282290 40695 25399 15296 261634 265 277 261634 226 231 226892 261634 79872 2069 1860 3 214491 81.98
1ng-30cycles-3_S52_L001_001 256766 300 301 256766 300 300 453161 223254 229907 58344 31485 26859 206824 257 272 206824 208 205 154532 206824 86516 1969 1688 3 137773 66.61
20ng-25cycles-3_S4_L001_001 296908 300 301 296908 300 300 549201 268361 280840 41730 25666 16064 260316 265 277 260316 226 231 226248 260316 86241 2126 1726 2 202205 77.68
zero5ng-30cycles-2_S75_L001_001 242911 300 301 242911 300 300 449556 221480 228076 33397 18562 14835 213997 267 278 213997 222 227 186286 213997 69094 1759 1455 3 168284 78.64
20ng-25cycles-2_S3_L001_001 269896 300 301 269896 300 300 497132 245483 251649 39492 21246 18246 235824 267 277 235824 221 225 203843 235824 82805 2068 1612 4 178385 75.64
20ng-20cycles-3_S16_L001_001 306702 300 301 306702 300 300 567042 275507 291535 42771 27605 15166 269014 265 277 269014 228 233 234694 269014 80070 2038 1839 3 222691 82.78
zero5ng-30cycles-3_S76_L001_001 132333 300 301 132333 300 300 183132 106023 77109 80943 25722 55221 65823 247 263 65823 174 177 29501 65823 23219 370 323 1 25229 38.33
20ng-20cycles-2_S15_L001_001 386487 300 301 386487 300 300 714269 350082 364187 53920 31621 22299 339401 266 277 339401 223 228 293514 339401 106564 2767 2482 3 275380 81.14
1ng-30cycles-2_S51_L001_001 391843 300 301 391843 300 300 724875 357756 367119 53718 28996 24722 345232 267 277 345232 221 226 299176 345232 117753 2869 2373 3 268610 77.81
5ng-25cycles-2_S27_L001_001 284620 300 301 284620 300 300 528610 259384 269226 36853 21459 15394 252210 267 277 252210 224 229 219794 252210 80454 2038 1683 1 201061 79.72
1ng-25cycles-1_S38_L001_001 133794 300 301 133794 300 300 245147 120830 124317 20848 11371 9477 115918 265 277 115918 220 223 98970 115918 39064 974 870 0 92208 79.55
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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 0.86 Firmicutes phylum 0.12 Clostridia class 0.06 Halanaerobiales order 0.03 Halanaerobiaceae family 0.03 Halothermothrix genus 0.01
OTU_10 - Root rootrank 1.0 Bacteria domain 0.97 Firmicutes phylum 0.18 Negativicutes class 0.05 Selenomonadales order 0.05 Veillonellaceae family 0.05 Thermosinus genus 0.01
OTU_11 Root rootrank 1.0 Archaea domain 0.31 "Crenarchaeota" phylum 0.19 Thermoprotei class 0.19 Thermoproteales order 0.18 Thermoproteaceae family 0.18 Thermocladium genus 0.17
OTU_12 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_13 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_14 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_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 0.21 "Euryarchaeota" phylum 0.2 Thermoplasmata class 0.18 Methanomassiliicoccales order 0.18 Methanomassiliicoccaceae family 0.18 Methanomassiliicoccus genus 0.18
OTU_17 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_18 - Root rootrank 1.0 Archaea domain 0.23 Pacearchaeota phylum 0.05 Pacearchaeota Incertae Sedis AR13 genus 0.05
OTU_19 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_20 Root rootrank 1.0 Bacteria domain 0.94 "Synergistetes" phylum 0.11 Synergistia class 0.11 Synergistales order 0.11 Synergistaceae family 0.11 Jonquetella genus 0.09
OTU_21 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 0.74
OTU_22 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_23 - 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_24 - Root rootrank 1.0 Bacteria domain 0.74 "Deinococcus-Thermus" phylum 0.03 Deinococci class 0.03 Thermales order 0.03 Thermaceae family 0.03 Marinithermus genus 0.03
OTU_25 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_26 - 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_27 Root rootrank 1.0 Bacteria domain 0.75 "Proteobacteria" phylum 0.33 Gammaproteobacteria class 0.28 Gammaproteobacteria_incertae_sedis order 0.19 Candidatus Carsonella genus 0.19
OTU_28 Root rootrank 1.0 Bacteria domain 0.99 "Planctomycetes" phylum 0.21 Planctomycetia class 0.21 Planctomycetales order 0.17 Planctomycetaceae family 0.17 Aquisphaera genus 0.07
OTU_29 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_30 Root rootrank 1.0 Bacteria domain 0.95 "Actinobacteria" phylum 0.07 Actinobacteria class 0.07 Coriobacteridae subclass 0.04 Coriobacteriales order 0.04 "Coriobacterineae" suborder 0.04 Coriobacteriaceae family 0.04 Adlercreutzia genus 0.01
OTU_31 - 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_32 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_33 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_34 - 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_35 Root rootrank 1.0 Bacteria domain 0.88 "Bacteroidetes" phylum 0.15 Cytophagia class 0.11 Cytophagales order 0.11 Cytophagaceae family 0.1 Nibribacter genus 0.08
OTU_36 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_37 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_38 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_39 - 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_40 Root rootrank 1.0 Archaea domain 0.4 "Euryarchaeota" phylum 0.24 Methanopyri class 0.1 Methanopyrales order 0.1 Methanopyraceae family 0.1 Methanopyrus genus 0.1
OTU_41 - 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_42 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Bacillaceae 2 family 0.81 Allobacillus genus 0.63
OTU_43 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_44 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Staphylococcaceae family 0.76 Staphylococcus genus 0.75
OTU_45 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_46 Root rootrank 1.0 Bacteria domain 0.88 "Bacteroidetes" phylum 0.29 "Bacteroidia" class 0.12 "Bacteroidales" order 0.12 "Bacteroidales"_incertae_sedis family 0.06 Phocaeicola genus 0.06
OTU_47 Root rootrank 1.0 Bacteria domain 0.97 Firmicutes phylum 0.27 Clostridia class 0.19 Clostridiales order 0.15 Peptococcaceae 2 family 0.04 Cryptanaerobacter genus 0.03
OTU_48 Root rootrank 1.0 Archaea domain 0.07 "Euryarchaeota" phylum 0.04 Thermoplasmata class 0.04 Methanomassiliicoccales order 0.04 Methanomassiliicoccaceae family 0.04 Methanomassiliicoccus genus 0.04
OTU_49 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_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 0.71 "Deinococcus-Thermus" phylum 0.08 Deinococci class 0.08 Thermales order 0.07 Thermaceae family 0.07 Vulcanithermus genus 0.05
OTU_52 - 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_53 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 0.08
OTU_54 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_55 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_56 - Root rootrank 1.0 Bacteria domain 0.85 "Bacteroidetes" phylum 0.16 Cytophagia class 0.12 Cytophagales order 0.12 Cytophagaceae family 0.11 Persicitalea genus 0.08
OTU_57 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 0.79
OTU_58 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.81 Bacillaceae 2 family 0.67 Terribacillus genus 0.35
OTU_59 - Root rootrank 1.0 Bacteria domain 0.88 Firmicutes phylum 0.15 Clostridia class 0.07 Clostridiales order 0.07 Clostridiaceae 1 family 0.04 Proteiniclasticum genus 0.04
OTU_60 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.87 Listeriaceae family 0.87 Listeria genus 0.87
OTU_61 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_62 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.99 Lactobacillaceae family 0.97 Lactobacillus genus 0.96
OTU_63 - Root rootrank 1.0 Bacteria domain 0.96 "Aquificae" phylum 0.05 Aquificae class 0.05 Aquificales order 0.05 Hydrogenothermaceae family 0.05 Venenivibrio genus 0.05
www/masque/done/file30a47fca2dc3/shaman_silva.biom
0 → 100644
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ed1db183
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:17:11","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Sphingomonas","s__Sphingomonas sp."]},{"id":"OTU_11","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria marthii"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Cyanobacteria","c__Melainabacteria","o__Obscuribacterales","f__Bacteria","g__Cyanobacteria","s__Melainabacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Brochothrix sp. TM5_5"]},{"id":"OTU_17","metadata":["k__Bacteria","p__Bacteroidetes","c__Bacteroidia","o__Bacteroidales","f__Muribaculaceae","g__Bacteria","s__Bacteroidetes"]},{"id":"OTU_18","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Bacteria"]},{"id":"OTU_19","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_2","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_20","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_21","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus fermentum"]},{"id":"OTU_22","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_23","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_24","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_25","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_26","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Escherichia coli"]},{"id":"OTU_27","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Escherichia coli"]},{"id":"OTU_28","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Terribacillus","s__Terribacillus aidingensis"]},{"id":"OTU_29","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__uncultured Bacillus sp."]},{"id":"OTU_3","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacillus acidicola"]},{"id":"OTU_30","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella sp."]},{"id":"OTU_31","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Betaproteobacteriales","f__Burkholderiaceae","g__Pelomonas","s__uncultured Comamonadaceae bacterium"]},{"id":"OTU_32","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus sp. 2011_Ileo_VSA_C5"]},{"id":"OTU_33","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus sp. 2011_Ileo_VSA_C5"]},{"id":"OTU_34","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Enterococcus faecalis"]},{"id":"OTU_35","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Staphylococcus aureus"]},{"id":"OTU_36","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Staphylococcus aureus"]},{"id":"OTU_37","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Enterococcus faecalis"]},{"id":"OTU_38","metadata":["k__Bacteria","p__Actinobacteria","c__Actinobacteria","o__Propionibacteriales","f__Propionibacteriaceae","g__Cutibacterium","s__Cutibacterium acnes"]},{"id":"OTU_39","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_4","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_40","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_41","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_42","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Bacteria"]},{"id":"OTU_43","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacillus sp. M29(2016b)"]},{"id":"OTU_44","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus fermentum"]},{"id":"OTU_45","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_46","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_47","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_48","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_49","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_5","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_50","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_51","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_52","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_53","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_54","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_55","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_56","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_57","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_58","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_59","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_6","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_60","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_61","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_62","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_63","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_7","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_8","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_9","metadata":["k__","p__","c__","o__","f__","g__","s__"]}],"columns":[{"id":"1ng.25cycles.1_S38_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.2_S39_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.3_S40_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.30cycles.1_S50_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.2_S51_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.3_S52_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"20ng.20cycles.1_S14_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.2_S15_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.3_S16_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.25cycles.1_S2_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.2_S3_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.3_S4_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.1_S26_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.2_S27_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.3_S28_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.1_S62_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.2_S63_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.3_S64_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.30cycles.1_S74_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.2_S75_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.3_S76_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}}],"data":[[17452,27133,22628,34080,44295,26503,37448,44573,39161,39050,32932,40607,25728,29573,31779,37086,38992,27499,43560,25485,6836],[13,0,12,22,3,5,18,18,11,24,1,12,37,0,22,22,4,16,43,8,3],[2,1,3,28,1,2,10,11,1,11,8,8,16,6,20,5,1,9,10,13,3],[11,29,14,55,74,41,35,48,20,45,75,62,49,65,41,18,43,19,52,52,4],[20,40,34,76,116,38,35,70,51,70,113,79,32,74,72,43,64,24,77,48,5],[0,6,3,8,9,8,0,0,0,0,0,0,0,3,0,12,18,5,13,6,0],[23,62,30,79,149,57,39,72,59,86,106,100,62,47,51,51,67,34,63,90,10],[0,2,0,4,4,0,6,3,2,5,3,1,1,2,6,1,0,2,9,5,0],[5,0,0,4,4,0,0,1,2,4,0,7,5,1,1,0,0,1,5,0,0],[3,1,0,14,4,0,4,4,9,2,6,4,6,5,3,1,0,1,8,5,2],[1,4,3,10,4,2,0,0,1,0,0,0,0,2,1,14,6,1,15,5,3],[15860,23646,22078,29667,43537,24072,36479,47320,38806,32012,25103,30496,26135,34793,32500,38523,42830,30774,39737,28634,4774],[0,0,0,0,5,1,1,0,2,1,0,5,4,0,0,0,1,1,7,0,0],[13,23,11,54,78,31,13,60,44,66,66,57,22,51,53,22,33,17,61,37,5],[10,17,12,34,56,32,14,23,18,55,38,49,20,36,16,13,32,6,53,21,7],[0,1,0,4,1,1,0,0,0,2,1,1,7,0,1,3,3,0,2,4,0],[0,0,0,3,0,2,0,3,7,2,0,0,4,0,1,3,0,0,2,2,0],[18,42,20,68,88,57,37,48,35,86,90,68,52,80,65,32,59,20,80,61,11],[1,1,1,7,1,0,0,0,1,0,0,0,5,1,0,2,2,0,3,1,0],[1,0,1,1,0,0,0,3,1,1,1,0,0,3,2,0,0,2,0,0,0],[0,0,0,2,0,1,0,0,0,0,0,1,0,2,0,1,0,0,1,2,0],[1,0,0,0,0,1,4,1,2,3,0,1,1,4,0,1,2,1,7,6,1],[13125,22105,17509,23529,36814,19721,30956,43056,33082,25061,23471,2612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\ No newline at end of file
www/masque/done/file30a47fca2dc3/shaman_silva_annotation.tsv
0 → 100644
View file @
ed1db183
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_13 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella Salmonella enterica
OTU_49 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp.
OTU_32 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Listeria marthii
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_31 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella Salmonella enterica subsp. enterica serovar Agona str. 47.E.09
OTU_36 Bacteria Cyanobacteria Melainabacteria Obscuribacterales
OTU_60 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Brochothrix sp. TM5_5
OTU_43 Bacteria Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae
OTU_12 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella
OTU_3 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Listeria monocytogenes
OTU_34 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Listeria monocytogenes