notebook.community

Edit and run

Goal

  • cluster in-silico amplicon sequences

Setting variables





In [1]:



    


import os
workDir = '/var/seq_data/ncbi_db/genome/Jan2016/rnammer_aln/'
ampliconFile = '/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.fna'

Init





In [2]:



    


%load_ext rpy2.ipython
%load_ext pushnote



    











In [3]:



    


%%R
library(dplyr)
library(tidyr)
library(ggplot2)



    


















    






/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: 
Attaching package: ‘dplyr’


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:stats’:

    filter, lag


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


  res = super(Function, self).__call__(*new_args, **new_kwargs)

















In [4]:



    


if not os.path.isdir(workDir):
    os.makedirs(workDir)
    
%cd $workDir



    


















    






/var/seq_data/ncbi_db/genome/Jan2016/rnammer_aln

Alignment-based QC





In [5]:



    


%%bash -s "$workDir"
# dowloading mothur silva databases

cd $1

if ! [ -d mothur_silva_db ]; then
    mkdir mothur_silva_db
fi

cd mothur_silva_db

if ! [ -e $1silva_ref_aln_mothur.fasta ]; then
    curl -o silva_Bac.zip http://www.mothur.org/w/images/9/98/Silva.bacteria.zip && unzip silva_Bac.zip
    curl -o silva_Euk.zip http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip && unzip silva_Euk.zip
    curl -o silva_Arc.zip http://www.mothur.org/w/images/3/3c/Silva.archaea.zip && unzip silva_Arc.zip
fi



    


















    






Archive:  silva_Bac.zip
   creating: silva.bacteria/
  inflating: silva.bacteria/.DS_Store  
   creating: __MACOSX/
   creating: __MACOSX/silva.bacteria/
  inflating: __MACOSX/silva.bacteria/._.DS_Store  
  inflating: silva.bacteria/silva.bacteria.fasta  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.fasta  
  inflating: silva.bacteria/silva.bacteria.gg.tax  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.gg.tax  
  inflating: silva.bacteria/silva.bacteria.ncbi.tax  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.ncbi.tax  
  inflating: silva.bacteria/silva.bacteria.rdp.tax  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.rdp.tax  
  inflating: silva.bacteria/silva.bacteria.rdp6.tax  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.rdp6.tax  
  inflating: silva.bacteria/silva.bacteria.silva.tax  
  inflating: __MACOSX/silva.bacteria/._silva.bacteria.silva.tax  
  inflating: silva.bacteria/silva.gold.ng.fasta  
  inflating: __MACOSX/._silva.bacteria  
Archive:  silva_Euk.zip
   creating: silva.eukarya/
  inflating: silva.eukarya/nogap.eukarya.fasta  
   creating: __MACOSX/silva.eukarya/
  inflating: __MACOSX/silva.eukarya/._nogap.eukarya.fasta  
  inflating: silva.eukarya/silva.eukarya.fasta  
  inflating: __MACOSX/silva.eukarya/._silva.eukarya.fasta  
  inflating: silva.eukarya/silva.eukarya.ncbi.tax  
  inflating: __MACOSX/silva.eukarya/._silva.eukarya.ncbi.tax  
  inflating: silva.eukarya/silva.eukarya.silva.tax  
  inflating: __MACOSX/silva.eukarya/._silva.eukarya.silva.tax  
  inflating: __MACOSX/._silva.eukarya  
Archive:  silva_Arc.zip
   creating: Silva.archaea/
  inflating: Silva.archaea/.silva.archaea.silva.tax.swp  
   creating: __MACOSX/Silva.archaea/
  inflating: __MACOSX/Silva.archaea/._.silva.archaea.silva.tax.swp  
  inflating: Silva.archaea/nogap.archaea.fasta  
  inflating: __MACOSX/Silva.archaea/._nogap.archaea.fasta  
  inflating: Silva.archaea/silva.archaea.fasta  
  inflating: __MACOSX/Silva.archaea/._silva.archaea.fasta  
  inflating: Silva.archaea/silva.archaea.gg.tax  
  inflating: Silva.archaea/silva.archaea.ncbi.tax  
  inflating: Silva.archaea/silva.archaea.rdp.tax  
  inflating: Silva.archaea/silva.archaea.silva.tax  
  inflating: __MACOSX/Silva.archaea/._silva.archaea.silva.tax  
  inflating: __MACOSX/._Silva.archaea  










    






  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 24.3M  100 24.3M    0     0  2420k      0  0:00:10  0:00:10 --:--:-- 2469k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2464k  100 2464k    0     0  2060k      0  0:00:01  0:00:01 --:--:-- 2062k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3773k  100 3773k    0     0  2185k      0  0:00:01  0:00:01 --:--:-- 2187k

















In [6]:



    


%%bash -s "$workDir"

cd $1'mothur_silva_db'

cat silva.bacteria/silva.bacteria.fasta \
    silva.eukarya/silva.eukarya.fasta \
    Silva.archaea/silva.archaea.fasta \
    > silva_ref_aln_mothur.fasta

printf "Number of sequences in mothur silva fasta: "
grep -c ">" silva_ref_aln_mothur.fasta



    


















    






Number of sequences in mothur silva fasta: 18491

















In [7]:



    


%%bash -s "$workDir"
# filtering column positions in silva db

cd $1'mothur_silva_db'

mothur "#filter.seqs(vertical=t, \
    fasta=silva_ref_aln_mothur.fasta, \
    processors=24)" > /dev/null

printf "Number of sequences post-filter: "
grep -c ">" silva_ref_aln_mothur.filter.fasta



    


















    






Number of sequences post-filter: 18491

Alignment of dataset to SILVA





In [11]:



    


silvaFile = os.path.join(workDir, 'mothur_silva_db', 'silva_ref_aln_mothur.filter.fasta')
cmd = 'mothur "#align.seqs(candidate={}, template={}, processors=20, flip=T)"'.format(ampliconFile, silvaFile)
!$cmd | tail -n 30



    


















    






400
500
600
700
752
100
200
300
400
500
600
700
750
100
200
300
400
500
600
700
751
It took 7 secs to align 15044 sequences.


Output File Names: 
/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.align
/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.align.report


mothur > quit()

















In [12]:



    


alnFile = os.path.splitext(ampliconFile)[0] + '.align'
cmd = 'mothur "#filter.seqs(fasta={}, vertical=t, processors=24)"'.format(alnFile)
!$cmd | tail -n 30



    


















    






600
627
100
200
300
400
500
600
627
100
200
300
400
500
600
627



Length of filtered alignment: 400
Number of columns removed: 11216
Length of the original alignment: 11616
Number of sequences used to construct filter: 15044

Output File Names: 
/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.filter
/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.fasta


mothur > quit()

















In [14]:



    


alnFiltFile = os.path.splitext(alnFile)[0] + '.filter.fasta'
cmd = 'mothur "#summary.seqs(fasta={}, processors=24)"'.format(alnFiltFile)
!$cmd | tail -n 25



    


















    






mothur > summary.seqs(fasta=/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.fasta, processors=24)

Using 24 processors.

mothur > summary.seqs(fasta=/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.fasta, processors=24)

Using 24 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	390	252	0	3	1
2.5%-tile:	5	390	252	0	4	377
25%-tile:	5	390	253	0	4	3762
Median: 	5	390	253	0	5	7523
75%-tile:	5	390	253	0	6	11284
97.5%-tile:	5	390	254	0	6	14668
Maximum:	7	400	262	0	8	15044
Mean:	4.9994	390.001	252.943	0	4.8735
# of Seqs:	15044

Output File Names: 
/var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.summary

It took 0 secs to summarize 15044 sequences.

mothur > quit()

Notes

  • alignment looks good

Usearch pipeline





In [15]:



    


# adding sequence 'size'; size=1 (no duplicate sequences)

alnFiltRnFile = os.path.splitext(alnFiltFile)[0] + '.rn.fna'
!perl -pe 's/[-.]+//g unless /^>/; s/(.+)/\$1;size=1/ if /^>/' \
    $alnFiltFile > $alnFiltRnFile

!head -n 4 $alnFiltRnFile



    


















    






>rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_5636180-5637670_DIR+;size=1
GACGGAGGAGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGTGGCCTATCAAGTCTGTTGTTAAAGCCCAGGGCTCAACTCTGGATCAGCAATGGAAACTGAAAGGCTAGAGTACGGTAGGGGTAGAGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCGTAACTGACACTCATGGACGAAAGCTAGGGGAGCGAAAGGG
>rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_1409155-1410645_DIR-;size=1
GACGGAGGAGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGTGGCCTATCAAGTCTGTTGTTAAAGCCCAGGGCTCAACTCTGGATCAGCAATGGAAACTGAAAGGCTAGAGTACGGTAGGGGTAGAGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCGTAACTGACACTCATGGACGAAAGCTAGGGGAGCGAAAGGG

















In [20]:



    


alnFiltRnSortFile = os.path.splitext(alnFiltRnFile)[0] + '_sorted.fna'
!usearch \
    -sortbysize $alnFiltRnFile \
    -output $alnFiltRnSortFile \
    -minsize 1
    
!head -n 10 $alnFiltRnSortFile
print '----------------------'
!tail -n 10 $alnFiltRnSortFile



    


















    






usearch v7.0.1090_i86linux32, 4.0Gb RAM (132Gb total), 40 cores
(C) Copyright 2013 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

Licensed to: chuck.peperanney@gmail.com

00:00 2.1Mb Reading /var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.rn.fna, 5.4Mb
00:00 7.6Mb 15044 (15.0k) seqs, min 252, avg 253, max 262nt
00:00 7.7Mb Getting sizes
00:00 7.9Mb Sorting 15044 sequences
00:00 7.9Mb  100.0% Writing /var/seq_data/ncbi_db/genome/Jan2016/rnammer/ssu_all.pcr.good.filter.rn_sorted.fna
>rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_742993-744530_DIR+;size=1
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTCTTTAAGTCTGATGTGAAAGCCC
ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAGAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG
AAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTG
GGGAGCAAACAGG
>rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3114313-3115850_DIR+;size=1
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTCTTTAAGTCTGATGTGAAAGCCC
ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAGAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG
AAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTG
GGGAGCAAACAGG
----------------------
>rRNA_NC_012526_Deinococcus_deserti_VCD115__Deinococcus_deserti_VCD115_16560-18053_DIR+;size=1
TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGGATGTTAAGTCTGGTTTTAAAGACT
GCGGCTCAACCGCAGGGATGGACTGGATACTGGCATTCTTGACCTCTGGAGAGGAAACCGGAATTCCTGGTGTAGCGGTG
GAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAGGTTTCTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTG
GGGAGCGAACCGG
>rRNA_NZ_CP011392_Dehalogenimonas_sp__WBC_2__Dehalogenimonas_sp__WBC_2_1248412-1249900_DIR-;size=1
TACGTAGGAGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGTGGGCGTAGGTGGTCTTTCAAGTCAGATGTGAAATCTC
CCGGCTTAACTGGGAGGGGTCATCTGATACTGTTGGACTTGAGTATGGCAGGAGAAAACGGAATTCCCGGTGTAGTGGTG
AAATGCGTAGATATCGGGAGGAACACCAGAGGCGAAGGCGGTTTTCTAGGCCAAAACTGACACTGAGGCCCGAAAGCGTG
GGGAGCGAACAGG

















In [21]:



    


otuFile = 'otus.fna'
!usearch \
    -cluster_otus $alnFiltRnSortFile \
    -otus $otuFile



    


















    






usearch v7.0.1090_i86linux32, 4.0Gb RAM (132Gb total), 40 cores
(C) Copyright 2013 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

Licensed to: chuck.peperanney@gmail.com

00:06  55Mb  100.0% 922 OTUs
                            
Input seqs  15044 (15.0k)
      OTUs  922
   Members  13610 (13.6k)
  Chimeras  512
   Max mem  55Mb
      Time  6.00s
Throughput  2507.3 seqs/sec.


















In [41]:



    


otuSnFile = os.path.splitext(otuFile)[0] + 'sn.fna'
cmd = '\'{print ">" "OTU" "." NR "::" $seq}\''
!bioawk -c fastx $cmd $otuFile | perl -pe 's/::/\n/g' > $otuSnFile
!head -n 4 $otuSnFile



    


















    






>OTU.1
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCgcgcgcAGGCGGTTCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAGAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG
>OTU.2
GACGGAGGAGGCAAGCGTTATCCGGAATCATTGGGCGTAAAGAGTCCGTAGGTGGCAACGCAAGTCGGCGGTCAAAGACCGGAGCTTAACTCCGGAGCGGCCGTGGAAACTGCGCAGCTAGAGTCCGGTAGGGGTAGCGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGAAGAACATCGGTGGCGAAAGCgcgcTACTGGGCCGGAACTGACACTGAGGGACGAAAGCTAGGGGAGCGAAAGGG

Mapping reads





In [42]:



    


!usearch \
        -usearch_global $alnFiltRnSortFile \
        -db $otuSnFile \
        -strand plus -id 0.97 \
        -blast6out otusn_map.txt \
        -threads 20



    


















    






usearch v7.0.1090_i86linux32, 4.0Gb RAM (132Gb total), 40 cores
(C) Copyright 2013 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

Licensed to: chuck.peperanney@gmail.com

00:00  19Mb Reading otussn.fna, 242.4kb
00:00  19Mb 922 seqs, min 252, avg 253, max 262nt
00:00  19Mb  100.0% Masking
00:00  19Mb  100.0% Word stats
00:00  21Mb  100.0% Building slots
00:00  21Mb  100.0% Build index
00:00 216Mb  100.0% Searching, 97.4% matched

















In [43]:



    


!head -n 4 otusn_map.txt



    


















    






rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_424242-425779_DIR+;size=1	OTU.1	100.0	253	0	0	1	253	1	253	*	*
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_836724-838261_DIR+;size=1	OTU.1	100.0	253	0	0	1	253	1	253	*	*
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3114313-3115850_DIR+;size=1	OTU.1	100.0	253	0	0	1	253	1	253	*	*
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3191594-3193131_DIR+;size=1	OTU.1	100.0	253	0	0	1	253	1	253	*	*

Making an index table linking genome_name --> OTU

  • genome_name -> seq_ID
  • seq_ID -> ssu_ID
  • ssu_ID -> OTU_ID




In [52]:



    


# genome_name -> seq_ID
!grep ">" ../bac_complete_rn/*fna | \
    perl -pe 's/.+bac_complete_rn\///; s/:>/\t/' > genome_seqID.txt
!head -n 4 genome_seqID.txt



    


















    






Acaryochloris_marina_MBIC11017.fna	NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017
Acetobacter_pasteurianus.fna	NZ_CP012111_Acetobacter_pasteurianus_strain_Ab3__Acetobacter_pasteurianus_str
Acetobacter_pasteurianus_386B.fna	NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B
Acetobacter_pasteurianus_IFO_3283-01-42C.fna	NC_017150_Acetobacter_pasteurianus_IFO_3283_01_42C_DNA__Acetobacter_pasteuria

















In [76]:



    


# genome_ID -> ssu_ID
!grep ">" ../rnammer/*.fna | \
    perl -ne 'print unless /ssu_all/' | \
    perl -pe 's/.+rnammer\///; s/\.fna:>/\t/; s/ .+//' > genomeID_ssuID.txt

!wc -l genomeID_ssuID.txt  
!head -n 4 genomeID_ssuID.txt



    


















    






15226 genomeID_ssuID.txt
Acaryochloris_marina_MBIC11017_rrn	rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_5636180-5637670_DIR+
Acaryochloris_marina_MBIC11017_rrn	rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_1409155-1410645_DIR-
Acetobacter_pasteurianus_386B_rrn	rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_1433628-1435103_DIR-
Acetobacter_pasteurianus_386B_rrn	rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_535312-536787_DIR-

Plotting number of taxa per OTU





In [114]:



    


%%R
df.idx = read.delim('genomeID_ssuID.txt', sep='\t', header=FALSE) %>%
    mutate(V1 = gsub('_rrn$', '.fna', V1))
colnames(df.idx) = c('genome_ID', 'ssu_ID')
df.idx %>% head



    


















    








                           genome_ID
1 Acaryochloris_marina_MBIC11017.fna
2 Acaryochloris_marina_MBIC11017.fna
3  Acetobacter_pasteurianus_386B.fna
4  Acetobacter_pasteurianus_386B.fna
5  Acetobacter_pasteurianus_386B.fna
6  Acetobacter_pasteurianus_386B.fna
                                                                                              ssu_ID
1 rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_5636180-5637670_DIR+
2 rRNA_NC_009925_Acaryochloris_marina_MBIC11017__Acaryochloris_marina_MBIC11017_1409155-1410645_DIR-
3   rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_1433628-1435103_DIR-
4     rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_535312-536787_DIR-
5   rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_1007960-1009435_DIR-
6   rRNA_NC_021991_Acetobacter_pasteurianus_386B__Acetobacter_pasteurianus_386B_1278576-1280053_DIR-


















In [115]:



    


%%R -w 900 -h 300
df = read.delim('otusn_map.txt', sep='\t', header=FALSE) %>%
    mutate(V1 = gsub(';size=[0-9]+', '', V1))

df.j = inner_join(df, df.idx, c('V1' = 'ssu_ID'))

df.j %>% head



    


















    








                                                                                            V1
1   rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_424242-425779_DIR+
2   rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_836724-838261_DIR+
3 rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3114313-3115850_DIR+
4 rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3191594-3193131_DIR+
5   rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_742993-744530_DIR+
6      rRNA_NC_022546_Plautia_stali_symbiont_DNA__Plautia_stali_symbiont_DNA_99747-101276_DIR+
       V2    V3  V4 V5 V6 V7  V8 V9 V10 V11 V12                     genome_ID
1   OTU.1 100.0 253  0  0  1 253  1 253   *   * Planococcus_sp_PAMC_21323.fna
2   OTU.1 100.0 253  0  0  1 253  1 253   *   * Planococcus_sp_PAMC_21323.fna
3   OTU.1 100.0 253  0  0  1 253  1 253   *   * Planococcus_sp_PAMC_21323.fna
4   OTU.1 100.0 253  0  0  1 253  1 253   *   * Planococcus_sp_PAMC_21323.fna
5   OTU.1 100.0 253  0  0  1 253  1 253   *   * Planococcus_sp_PAMC_21323.fna
6 OTU.467  97.6 253  6  0  1 253  1 253   *   *    Plautia_stali_symbiont.fna


















In [116]:



    


%%R -w 900 -h 300
# check: number of OTUs per genome should be 1 (unless outlier ssu genes in genome)
df.multotu = df.j %>%
    distinct(genome_ID, V2) %>%
    group_by(genome_ID) %>%
    mutate(n=n()) %>%
    ungroup() %>%
    filter(n > 1) 

df.multotu %>% nrow %>% print
df.multotu %>% head %>% as.data.frame



    


















    








[1] 116
                                                                                                       V1
1                 rRNA_NC_022546_Plautia_stali_symbiont_DNA__Plautia_stali_symbiont_DNA_99747-101276_DIR+
2                rRNA_NC_022546_Plautia_stali_symbiont_DNA__Plautia_stali_symbiont_DNA_323956-325340_DIR+
3 rRNA_NC_018525_Pectobacterium_carotovorum_subsp__carotovorum_PCC21__Pectobacterium_3793986-3795513_DIR-
4 rRNA_NC_018525_Pectobacterium_carotovorum_subsp__carotovorum_PCC21__Pectobacterium_4837895-4839423_DIR+
5                                rRNA_NC_014837_Pantoea_sp__At_9b__Pantoea_sp__At_9b_3951563-3953092_DIR-
6                                  rRNA_NC_014837_Pantoea_sp__At_9b__Pantoea_sp__At_9b_908002-909532_DIR+
       V2    V3  V4 V5 V6 V7  V8 V9 V10 V11 V12
1 OTU.467  97.6 253  6  0  1 253  1 253   *   *
2   OTU.3  97.6 253  6  0  1 253  1 253   *   *
3  OTU.66 100.0 253  0  0  1 253  1 253   *   *
4  OTU.12  97.2 253  7  0  1 253  1 253   *   *
5   OTU.3  98.0 253  5  0  1 253  1 253   *   *
6  OTU.66  97.6 254  5  1  1 254  1 253   *   *
                                               genome_ID n
1                             Plautia_stali_symbiont.fna 2
2                             Plautia_stali_symbiont.fna 2
3 Pectobacterium_carotovorum_subsp_carotovorum_PCC21.fna 2
4 Pectobacterium_carotovorum_subsp_carotovorum_PCC21.fna 2
5                                   Pantoea_sp_At-9b.fna 2
6                                   Pantoea_sp_At-9b.fna 2


















In [117]:



    


%%R -w 900 -h 300
df.j.s = df.j %>%
    group_by(V2) %>%
    summarize(n_genomes=n()) %>%
    ungroup()

df.j.s$V2 = reorder(df.j.s$V2, -df.j.s$n_genomes)

ggplot(df.j.s %>% distinct(V2), aes(V2, n_genomes)) +
    geom_point() +
    theme_bw() +
    labs(x='OTU', y='Number of genomes in OTU') +
    theme(
        axis.text.x = element_blank()
    )



    


















    
























In [118]:



    


%%R -w 900 -h 300
# OTUs that are not singletons
df.j.s = df.j %>%
    group_by(V2) %>%
    summarize(n_genomes=n()) %>%
    ungroup() %>%
    filter(n_genomes > 1)

df.j.s$V2 = reorder(df.j.s$V2, -df.j.s$n_genomes)

ggplot(df.j.s %>% distinct(V2), aes(V2, n_genomes)) +
    geom_point() +
    labs(x='OTU', y='Number of genomes in OTU') +
    theme_bw() +
    theme(
        axis.text.x = element_blank()
    )



    


















    
























In [119]:



    


%%R
# OTUs that are not singletons
df.ns = df.j %>%
    group_by(V2) %>%
    mutate(n_genomes=n()) %>%
    ungroup() %>%
    filter(n_genomes > 1)

# status
cat('Number of non-singleton OTUs:', df.ns %>% distinct(V2) %>% nrow, '\n')

# writing table
outFile = 'otusn_map_nonSingle.txt'
write.table(df.ns, outFile, sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE)



    


















    








Number of non-singleton OTUs: 794 


















In [120]:



    


!head -n 5 otusn_map_nonSingle.txt



    


















    






rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_424242-425779_DIR+	OTU.1	100	253	0	0	1	253	1	253	*	*	Planococcus_sp_PAMC_21323.fna	39
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_836724-838261_DIR+	OTU.1	100	253	0	0	1	253	1	253	*	*	Planococcus_sp_PAMC_21323.fna	39
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3114313-3115850_DIR+	OTU.1	100	253	0	0	1	253	1	253	*	*	Planococcus_sp_PAMC_21323.fna	39
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_3191594-3193131_DIR+	OTU.1	100	253	0	0	1	253	1	253	*	*	Planococcus_sp_PAMC_21323.fna	39
rRNA_NZ_CP009129_Planococcus_sp__PAMC_21323__Planococcus_sp__PAMC_21323_742993-744530_DIR+	OTU.1	100	253	0	0	1	253	1	253	*	*	Planococcus_sp_PAMC_21323.fna	39

What's in the really big OTU?





In [121]:



    


%%R
bigOTU = df.j.s[df.j.s$n_genomes == max(df.j.s$n_genomes),][1,'V2'] %>% as.matrix %>% as.character
df.j %>%
    filter(V2 == bigOTU) %>%
    select(genome_ID)



    


















    








                                                                               genome_ID
1                                                            Pluralibacter_gergoviae.fna
2                                                            Pluralibacter_gergoviae.fna
3                                                             Plautia_stali_symbiont.fna
4                                                            Pluralibacter_gergoviae.fna
5                                                            Pluralibacter_gergoviae.fna
6                                                            Pluralibacter_gergoviae.fna
7                                                            Pluralibacter_gergoviae.fna
8                                                            Pluralibacter_gergoviae.fna
9                                                                   Pantoea_sp_At-9b.fna
10                                                                  Pantoea_sp_At-9b.fna
11                                                                  Pantoea_sp_At-9b.fna
12                                                                  Pantoea_sp_At-9b.fna
13                                                                  Pantoea_sp_At-9b.fna
14                                                        Raoultella_ornithinolytica.fna
15                                                        Raoultella_ornithinolytica.fna
16                                                        Raoultella_ornithinolytica.fna
17                                                        Raoultella_ornithinolytica.fna
18                                                        Raoultella_ornithinolytica.fna
19                                                        Raoultella_ornithinolytica.fna
20                                                        Raoultella_ornithinolytica.fna
21                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
22                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
23                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
24                                                        Raoultella_ornithinolytica.fna
25                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
26                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
27                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
28                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
29                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
30                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
31                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
32                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
33                 Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
34                                                Salmonella_enterica_subsp_enterica.fna
35                                                Salmonella_enterica_subsp_enterica.fna
36                 Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
37                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
38                                                Salmonella_enterica_subsp_enterica.fna
39                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
40                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
41                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
42                   Salmonella_enterica_subsp_arizonae_serovar_62:z36:-_str_RKS2983.fna
43                                                Salmonella_enterica_subsp_enterica.fna
44                 Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
45                                                Salmonella_enterica_subsp_enterica.fna
46                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
47                                                Salmonella_enterica_subsp_enterica.fna
48                                                Salmonella_enterica_subsp_enterica.fna
49                                                        Salmonella_bongori_N268-08.fna
50                                                        Salmonella_bongori_N268-08.fna
51                 Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
52                            Salmonella_enterica_subsp_arizonae_serovar_62:z4_z23:-.fna
53                                                        Salmonella_bongori_N268-08.fna
54                                                     Salmonella_bongori_NCTC_12419.fna
55                                                     Salmonella_bongori_NCTC_12419.fna
56                                                        Salmonella_bongori_N268-08.fna
57                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
58                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
59                                  Salmonella_bongori_serovar_48:z41:--_str_RKS3044.fna
60                                                     Salmonella_bongori_NCTC_12419.fna
61                                                     Salmonella_bongori_NCTC_12419.fna
62                 Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
63                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
64                                                     Salmonella_bongori_NCTC_12419.fna
65                                                        Salmonella_bongori_N268-08.fna
66                                                        Salmonella_bongori_N268-08.fna
67                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
68               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
69               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
70               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
71                                                     Salmonella_bongori_NCTC_12419.fna
72                                                        Salmonella_bongori_N268-08.fna
73                   Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
74                                                     Salmonella_bongori_NCTC_12419.fna
75                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
76                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
77               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
78                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
79        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
80        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
81        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
82               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
83                 Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
84        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
85        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
86                 Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
87                 Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
88        Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
89                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
90               Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
91                        Salmonella_enterica_subsp_enterica_serovar_Agona_str_SL483.fna
92              Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
93                 Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
94                 Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
95                         Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
96                         Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
97              Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
98              Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
99              Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
100                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
101                Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
102                        Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
103                        Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
104                        Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
105                Salmonella_enterica_subsp_enterica_serovar_Anatum_str_CDC_06-0532.fna
106              Salmonella_enterica_subsp_enterica_serovar_Anatum_str_ATCC_BAA-1592.fna
107             Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
108                Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
109                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
110                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
111                Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
112                Salmonella_enterica_subsp_enterica_serovar_4_5_12:i:-_str_08-1736.fna
113             Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
114             Salmonella_enterica_subsp_enterica_serovar_Abaetetuba_str_ATCC_35640.fna
115                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
116                        Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
117                        Salmonella_enterica_subsp_enterica_serovar_Abony_str_0014.fna
118                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
119                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
120                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
121                  Salmonella_enterica_subsp_enterica_serovar_Agona_str_460004_2-1.fna
122                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
123                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
124                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
125                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
126                       Salmonella_enterica_subsp_enterica_serovar_Agona_str_24249.fna
127                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
128                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
129                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
130                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
131                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
132                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
133                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
134                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
135                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
136                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
137                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
138                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
139                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
140                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
141                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
142                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
143                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
144                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
145                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
146                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
147                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
148                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
149                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
150                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
151                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
152                 Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT104.fna
153                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
154                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
155                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
156                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
157                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
158                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
159                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
160                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
161                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
162                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
163                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
164                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
165        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
166                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
167        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
168                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
169                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
170                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
171        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
172                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
173        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
174        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
175                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
176                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
177                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2.fna
178        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
179        Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_CDC_2011K-0870.fna
180  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
181  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
182  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
183  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
184  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
185                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
186                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580.fna
187  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
188                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
189                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
190                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
191    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
192                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
193                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
194                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_L-3553.fna
195                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
196                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
197                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_798.fna
198                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
199    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
200  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_USDA-ARS-USMARC-1899.fna
201                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
202                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
203                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
204    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
205                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
206    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
207                           Salmonella_enterica_subsp_enterica_serovar_Weltevreden.fna
208                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
209                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
210                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
211    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
212    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
213                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
214                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
215                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
216                   Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2.fna
217                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
218                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
219                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
220                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
221                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
222                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
223                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
224                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
225                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_SL1344.fna
226                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
227               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
228               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
229               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
230                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
231               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
232                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
233                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
234                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_UK-1.fna
235                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
236                Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_ST4_74.fna
237               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
238               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
239                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
240                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
241                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
242    Salmonella_enterica_subsp_enterica_serovar_Typhimurium_var_5-_str_CFSAN001921.fna
243                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
244                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
245                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
246                  Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_U288.fna
247                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
248               Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_T000240.fna
249                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
250                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
251                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
252                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
253                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
254                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
255             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
256               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
257               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
258             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
259           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
260             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
261             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
262           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
263           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
264             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
265             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
266             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
267                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
268             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
269             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
270             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
271             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
272           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
273                   Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_S06004.fna
274           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
275           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
276           Salmonella_enterica_subsp_enterica_serovar_Schwarzengrund_str_CVM19633.fna
277             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
278                Salmonella_enterica_subsp_enterica_serovar_Pullorum_str_ATCC_9120.fna
279                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
280                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
281                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
282               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
283             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
284             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
285               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
286               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
287                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
288             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
289                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
290               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
291             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
292             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
293               Salmonella_enterica_subsp_enterica_serovar_Paratyphi_C_str_RKS4594.fna
294                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
295                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
296                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
297             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
298             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601.fna
299                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
300                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
301                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
302                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
303                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
304                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
305                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
306                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
307                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
308                  Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7.fna
309             Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150.fna
310                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
311                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
312                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
313                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
314                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
315                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
316                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
317                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
318                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
319                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
320                           Salmonella_enterica_subsp_enterica_serovar_Typhimurium.fna
321             Salmonella_enterica_subsp_enterica_serovar_Sloterdijk_str_ATCC_15791.fna
322                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
323                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
324                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
325                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
326                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
327                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
328                       Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty21a.fna
329                    Salmonella_enterica_subsp_enterica_serovar_Typhi_str_P-stx-12.fna
330                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
331                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
332          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
333                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
334                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
335                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
336          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
337          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
338                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
339          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
340                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
341                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
342                        Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18.fna
343          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
344                              Salmonella_enterica_subsp_enterica_serovar_Thompson.fna
345                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
346                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
347                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
348                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
349                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
350                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
351                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
352                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
353                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
354                Salmonella_enterica_subsp_enterica_serovar_Thompson_str_ATCC_8391.fna
355          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
356                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
357                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
358          Salmonella_enterica_subsp_enterica_serovar_Tennessee_str_TXSC_TXSC08-19.fna
359                         Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2.fna
360                   Salmonella_enterica_subsp_enterica_serovar_Thompson_str_RM6836.fna
361            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
362            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
363            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
364            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
365            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
366            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
367            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
368            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
369            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
370            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
371            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
372            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
373            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
374            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
375            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
376            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
377            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
378            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
379            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
380            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
381            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110221.fna
382            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
383            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
384            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
385            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
386            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
387            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
388            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110223.fna
389            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
390            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090884.fna
391            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
392            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
393            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
394            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
395            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090884.fna
396            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
397            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
398            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
399            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
400            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090884.fna
401            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
402            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090884.fna
403            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
404            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
405            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
406            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
407            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100134.fna
408            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
409            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
410            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100103.fna
411            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100103.fna
412            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
413            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100103.fna
414            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100130.fna
415            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
416            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
417            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
418            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
419            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
420            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
421            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
422            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
423            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100101.fna
424            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100103.fna
425            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
426            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
427            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
428            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110353.fna
429            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
430            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
431            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
432            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
433            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
434            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
435            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
436            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
437            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
438            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20100103.fna
439            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
440            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110359.fna
441            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
442            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
443            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110360.fna
444            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
445            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
446            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111095.fna
447            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
448            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
449            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
450            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
451            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
452            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
453            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
454            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
455            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
456            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
457            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
458            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
459            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
460            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
461            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
462            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
463            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
464            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
465            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
466            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
467            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
468            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
469            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
470            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110356.fna
471            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110361.fna
472            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110355.fna
473               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
474               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
475            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
476            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
477               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
478               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
479            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110357.fna
480            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
481           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
482           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
483            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110354.fna
484               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
485           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
486           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
487               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
488               Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC-B67.fna
489           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
490           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
491                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
492                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
493                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
494                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
495                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
496                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
497                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
498                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
499                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
500                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
501              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
502                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
503                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
504            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20110358.fna
505           Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_ATCC_10708.fna
506                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
507                Salmonella_enterica_subsp_enterica_serovar_Cubana_str_CFSAN002050.fna
508                Salmonella_enterica_subsp_enterica_serovar_Dublin_str_CT_02021853.fna
509       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
510       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
511              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
512              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
513       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1175.fna
514       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
515                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
516       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
517       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
518       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
519              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
520              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
521                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
522                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
523              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
524              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
525              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
526              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
527              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
528                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
529                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
530              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
531              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
532                          Salmonella_enterica_subsp_enterica_serovar_Choleraesuis.fna
533            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
534            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
535              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
536              Salmonella_enterica_subsp_enterica_serovar_Bredeney_str_CFSAN001080.fna
537            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
538            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
539              Salmonella_enterica_subsp_enterica_serovar_Bareilly_str_CFSAN000189.fna
540       Salmonella_enterica_subsp_enterica_serovar_Anatum_str_USDA-ARS-USMARC-1735.fna
541            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090135.fna
542            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
543            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
544            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
545            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
546            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090135.fna
547            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
548            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
549            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
550            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
551            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
552            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
553            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
554            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
555            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
556            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
557            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
558            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
559            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
560            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
561            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090193.fna
562            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090332.fna
563                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
564                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
565                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
566                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
567                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
568                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
569            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090531.fna
570                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
571               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
572                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
573                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
574                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
575                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
576            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090641.fna
577            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090698.fna
578        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
579        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
580        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
581        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
582            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090135.fna
583            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090135.fna
584               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
585        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
586               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
587                 Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_18569.fna
588               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
589                           Salmonella_enterica_subsp_enterica_serovar_Enteritidis.fna
590               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
591               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
592                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
593                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
594            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
595        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
596        Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_CDC_2010K_0968.fna
597            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
598            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
599                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
600                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
601                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
602                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
603            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20090135.fna
604                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
605                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
606                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
607                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
608                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
609                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
610                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
611            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
612            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
613            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
614                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
615                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
616                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
617              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
618               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
619              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
620                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
621                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21538.fna
622            Salmonella_enterica_subsp_enterica_serovar_Newport_str_CDC_2010K-2159.fna
623                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
624                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
625               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_77-1427.fna
626                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
627              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
628              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
629               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
630              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
631              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
632                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_21550.fna
633                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22425.fna
634               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
635               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
636   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
637              Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_507440-20.fna
638   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
639   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
640   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
641   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
642   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
643   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
644   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
645   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
646               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
647               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
648               Salmonella_enterica_subsp_enterica_serovar_Javiana_str_CFSAN001992.fna
649      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
650      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
651      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
652            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
653   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
654                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
655   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
656   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1921.fna
657            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
658            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
659                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
660      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
661                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
662   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
663      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
664                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
665                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
666                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
667                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
668                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
669      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
670            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
671            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
672                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
673                           Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A.fna
674            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
675                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
676                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
677                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
678                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
679                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
680                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
681                  Salmonella_enterica_subsp_enterica_serovar_Panama_str_ATCC_7378.fna
682   Salmonella_enterica_subsp_enterica_serovar_Montevideo_str_USDA-ARS-USMARC-1903.fna
683                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
684                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
685                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
686                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
687                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
688                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
689                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
690                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
691                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
692                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
693                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
694                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
695                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
696                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
697            Salmonella_enterica_subsp_enterica_serovar_Newport_str_USMARC-S3124_1.fna
698      Salmonella_enterica_subsp_enterica_serovar_Newport_str_USDA-ARS-USMARC-1927.fna
699                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
700                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
701                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
702                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
703                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N1543.fna
704                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22462.fna
705                 Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_22513.fna
706                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
707                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
708            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120929.fna
709            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
710            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
711            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
712            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
713                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
714                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
715                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
716            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
717            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
718            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120916.fna
719            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
720            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
721            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
722                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
723            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
724            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
725                     Salmonella_enterica_subsp_enterica_serovar_Newport_str_SL254.fna
726                Salmonella_enterica_subsp_enterica_serovar_Newport_str_CVM_N18486.fna
727            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
728            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
729            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
730               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
731            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
732            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
733               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
734               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
735            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
736            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
737               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
738            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
739            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
740            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20121175.fna
741               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
742            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
743            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
744            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
745            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
746            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
747            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
748            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
749            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
750            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
751            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111175.fna
752            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
753            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20111174.fna
754            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
755            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
756            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
757            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
758            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120008.fna
759            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
760               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
761            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
762            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_SA20093266.fna
763               Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_P125109.fna
764            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
765            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
766            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
767            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
768            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
769            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
770            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
771            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120005.fna
772            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
773            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
774            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
775            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
776            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
777                   Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_B182.fna
778            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
779            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
780            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
781    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
782            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
783                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
784                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
785                   Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_B182.fna
786                   Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_B182.fna
787            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
788                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
789                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
790                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
791                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
792                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
793            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
794                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
795            Salmonella_enterica_subsp_enterica_serovar_Enteritidis_str_EC20120002.fna
796       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
797                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
798       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
799                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
800    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
801    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
802    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
803    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
804                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
805                              Salmonella_enterica_subsp_enterica_serovar_Infantis.fna
806       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
807       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
808       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
809       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
810                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
811    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
812    Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_CDC1983-67.fna
813                   Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_B182.fna
814                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
815                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
816                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_SL476.fna
817            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002064.fna
818                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
819                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
820       Salmonella_enterica_subsp_enterica_serovar_Gallinarum_pullorum_str_RKS5078.fna
821                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
822                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
823                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
824                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
825                 Salmonella_enterica_subsp_enterica_serovar_Gallinarum_str_287_91.fna
826                   Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_B182.fna
827                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
828            Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069.fna
829                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
830                  Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_41578.fna
831                                                                   Cedecea_neteri.fna
832                                                                   Cedecea_neteri.fna
833                                                                   Cedecea_neteri.fna
834                                                                   Cedecea_neteri.fna
835                                                                   Cedecea_neteri.fna
836                                                                   Cedecea_neteri.fna
837                                                                   Cedecea_neteri.fna
838                                                  Chania_multitudinisentens_RB-25.fna
839                                                  Chania_multitudinisentens_RB-25.fna
840                                                  Chania_multitudinisentens_RB-25.fna
841                                                  Chania_multitudinisentens_RB-25.fna
842                                                  Chania_multitudinisentens_RB-25.fna
843                                                  Chania_multitudinisentens_RB-25.fna
844                                                  Chania_multitudinisentens_RB-25.fna
845                                                        Erwinia_pyrifoliae_Ep1_96.fna
846                                                        Erwinia_pyrifoliae_Ep1_96.fna
847                                                        Erwinia_pyrifoliae_Ep1_96.fna
848                                                        Erwinia_pyrifoliae_Ep1_96.fna
849                                                        Erwinia_pyrifoliae_Ep1_96.fna
850                                                        Erwinia_pyrifoliae_Ep1_96.fna
851                                                        Erwinia_pyrifoliae_Ep1_96.fna
852                                                      Erwinia_tasmaniensis_Et1_99.fna
853                                                      Erwinia_tasmaniensis_Et1_99.fna
854                                                      Erwinia_tasmaniensis_Et1_99.fna
855                                                      Erwinia_tasmaniensis_Et1_99.fna
856                                                      Erwinia_tasmaniensis_Et1_99.fna
857                                                      Erwinia_tasmaniensis_Et1_99.fna
858                                                         Erwinia_billingiae_Eb661.fna
859                                                      Erwinia_tasmaniensis_Et1_99.fna
860                                                                Erwinia_sp_Ejp617.fna
861                                                                Erwinia_sp_Ejp617.fna
862                                                         Klebsiella_michiganensis.fna
863                                                         Klebsiella_michiganensis.fna
864                                                         Klebsiella_michiganensis.fna
865                                                         Klebsiella_michiganensis.fna
866                                                               Klebsiella_oxytoca.fna
867                                                               Klebsiella_oxytoca.fna
868                                                               Klebsiella_oxytoca.fna
869                                                               Klebsiella_oxytoca.fna
870                                                               Klebsiella_oxytoca.fna
871                                                               Klebsiella_oxytoca.fna
872                                                               Klebsiella_oxytoca.fna
873                                                        Klebsiella_oxytoca_KONIH1.fna
874                                                        Klebsiella_oxytoca_KONIH1.fna
875                                                        Klebsiella_oxytoca_KONIH1.fna
876                                                        Klebsiella_oxytoca_KONIH1.fna
877                                                               Klebsiella_oxytoca.fna
878                                                        Klebsiella_oxytoca_KONIH1.fna
879                                                        Klebsiella_oxytoca_KONIH1.fna
880                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
881                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
882                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
883                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
884                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
885                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
886                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
887                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
888                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
889                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
890                                            Klebsiella_pneumoniae_30684_NJST258_2.fna
891                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
892                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
893                                                          Klebsiella_oxytoca_E718.fna
894                                                          Klebsiella_oxytoca_E718.fna
895                                                        Klebsiella_oxytoca_HKOPL1.fna
896                                                          Klebsiella_oxytoca_E718.fna
897                                            Klebsiella_pneumoniae_30660_NJST258_1.fna
898                                                        Klebsiella_oxytoca_HKOPL1.fna
899                                                        Klebsiella_oxytoca_HKOPL1.fna
900                                                          Klebsiella_oxytoca_E718.fna
901                                                          Klebsiella_oxytoca_E718.fna
902                                                         Klebsiella_michiganensis.fna
903                                                          Klebsiella_oxytoca_E718.fna
904                                                          Klebsiella_oxytoca_E718.fna
905                                                          Klebsiella_oxytoca_E718.fna
906                                                        Klebsiella_oxytoca_HKOPL1.fna
907                                                     Klebsiella_oxytoca_KCTC_1686.fna
908                                                     Klebsiella_oxytoca_KCTC_1686.fna
909                                                     Klebsiella_oxytoca_KCTC_1686.fna
910                                                     Klebsiella_oxytoca_KCTC_1686.fna
911                                                        Klebsiella_oxytoca_HKOPL1.fna
912                                                        Klebsiella_oxytoca_HKOPL1.fna
913                                                     Klebsiella_oxytoca_KCTC_1686.fna
914                                                     Klebsiella_oxytoca_KCTC_1686.fna
915                                                        Klebsiella_oxytoca_HKOPL1.fna
916                                                        Klebsiella_oxytoca_HKOPL1.fna
917                                                     Klebsiella_oxytoca_KCTC_1686.fna
918                                                         Klebsiella_michiganensis.fna
919                                                        Klebsiella_oxytoca_KONIH1.fna
920                                                     Klebsiella_oxytoca_KCTC_1686.fna
921                                                         Klebsiella_michiganensis.fna
922                                                        Klebsiella_oxytoca_KONIH1.fna
923                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
924                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
925                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
926                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
927                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
928                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
929                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
930                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
931                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
932                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
933                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
934                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
935                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
936                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
937                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
938                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
939                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
940                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
941                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
942                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
943                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
944                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
945                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
946                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
947                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
948                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
949                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
950                                    Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
951                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
952                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
953                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
954                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
955                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
956                                    Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
957                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
958                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
959                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
960                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
961                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
962                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
963                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
964                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
965                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
966                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
967                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
968                                      Klebsiella_pneumoniae_subsp_pneumoniae_Kp13.fna
969                                 Klebsiella_pneumoniae_subsp_pneumoniae_PittNDM01.fna
970                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
971                                    Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
972                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH24.fna
973                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
974                                Klebsiella_pneumoniae_subsp_pneumoniae_NTUH-K2044.fna
975                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH27.fna
976                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPR0928.fna
977                                                              Kluyvera_intermedia.fna
978                                                              Kluyvera_intermedia.fna
979                                                           Kosakonia_sacchari_SP1.fna
980                                 Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578.fna
981                                                           Kosakonia_sacchari_SP1.fna
982                                                           Kosakonia_sacchari_SP1.fna
983                                                           Kosakonia_sacchari_SP1.fna
984                                                           Kosakonia_sacchari_SP1.fna
985                                                           Kosakonia_sacchari_SP1.fna
986                                                           Kosakonia_sacchari_SP1.fna
987                                                       Klebsiella_variicola_At-22.fna
988                                                       Klebsiella_variicola_At-22.fna
989                                                       Klebsiella_variicola_At-22.fna
990                                           Klebsiella_pneumoniae_subsp_pneumoniae.fna
991                                                       Klebsiella_variicola_At-22.fna
992                                                       Klebsiella_variicola_At-22.fna
993                                           Klebsiella_pneumoniae_subsp_pneumoniae.fna
994                                           Klebsiella_pneumoniae_subsp_pneumoniae.fna
995                                                       Klebsiella_variicola_At-22.fna
996                                           Klebsiella_pneumoniae_subsp_pneumoniae.fna
997                                           Klebsiella_pneumoniae_subsp_pneumoniae.fna
998                                                       Klebsiella_variicola_At-22.fna
999                                                              Kluyvera_intermedia.fna
1000                                                            Klebsiella_variicola.fna
1001                                                             Kluyvera_intermedia.fna
1002                                                            Klebsiella_variicola.fna
1003                                                      Klebsiella_variicola_At-22.fna
1004                                          Klebsiella_pneumoniae_subsp_pneumoniae.fna
1005                                                             Kluyvera_intermedia.fna
1006                                                            Klebsiella_variicola.fna
1007                                                            Klebsiella_variicola.fna
1008                                                            Klebsiella_variicola.fna
1009                                                            Klebsiella_variicola.fna
1010                                                            Klebsiella_variicola.fna
1011                                                     Klebsiella_pneumoniae_HK787.fna
1012                                                     Klebsiella_pneumoniae_HK787.fna
1013                                                     Klebsiella_pneumoniae_HK787.fna
1014                                                             Kluyvera_intermedia.fna
1015                                                   Klebsiella_pneumoniae_DMC1097.fna
1016                                                     Klebsiella_pneumoniae_HK787.fna
1017                                                   Klebsiella_pneumoniae_DMC1097.fna
1018                                                             Kluyvera_intermedia.fna
1019                                                      Klebsiella_pneumoniae_JM45.fna
1020                                                     Klebsiella_pneumoniae_HK787.fna
1021                                                     Klebsiella_pneumoniae_HK787.fna
1022                                                      Klebsiella_pneumoniae_JM45.fna
1023                                                     Klebsiella_pneumoniae_HK787.fna
1024                                                      Klebsiella_pneumoniae_JM45.fna
1025                                                     Klebsiella_pneumoniae_HK787.fna
1026                                                   Klebsiella_pneumoniae_UHKPC07.fna
1027                                                 Klebsiella_pneumoniae_KCTC_2242.fna
1028                                                      Klebsiella_pneumoniae_JM45.fna
1029                                                      Klebsiella_pneumoniae_JM45.fna
1030                                                   Klebsiella_pneumoniae_DMC1097.fna
1031                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
1032                                                            Klebsiella_variicola.fna
1033                                                 Klebsiella_pneumoniae_KCTC_2242.fna
1034                                                      Klebsiella_pneumoniae_JM45.fna
1035                                                      Klebsiella_pneumoniae_JM45.fna
1036                                                       Klebsiella_pneumoniae_342.fna
1037                                           Klebsiella_pneumoniae_30684_NJST258_2.fna
1038                                                  Klebsiella_pneumoniae_500_1420.fna
1039                                                  Klebsiella_pneumoniae_500_1420.fna
1040                                                       Klebsiella_pneumoniae_342.fna
1041                                                       Klebsiella_pneumoniae_342.fna
1042                                                       Klebsiella_pneumoniae_342.fna
1043                                                       Klebsiella_pneumoniae_342.fna
1044                                                      Klebsiella_pneumoniae_CG43.fna
1045                                                  Klebsiella_pneumoniae_500_1420.fna
1046                                                      Klebsiella_pneumoniae_JM45.fna
1047                                                 Klebsiella_pneumoniae_KCTC_2242.fna
1048                                                       Klebsiella_pneumoniae_342.fna
1049                                                  Klebsiella_pneumoniae_500_1420.fna
1050                                                   Klebsiella_pneumoniae_DMC1097.fna
1051                                                   Klebsiella_pneumoniae_DMC1097.fna
1052                                                      Klebsiella_pneumoniae_CG43.fna
1053                                                      Klebsiella_pneumoniae_CG43.fna
1054                                                      Klebsiella_pneumoniae_CG43.fna
1055                                                  Klebsiella_pneumoniae_500_1420.fna
1056                                                      Klebsiella_pneumoniae_CG43.fna
1057                                                  Klebsiella_pneumoniae_500_1420.fna
1058                                                   Klebsiella_pneumoniae_DMC1097.fna
1059                                                   Klebsiella_pneumoniae_DMC1097.fna
1060                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1061                                                       Klebsiella_pneumoniae_342.fna
1062                                                      Klebsiella_pneumoniae_CG43.fna
1063                                                      Klebsiella_pneumoniae_CG43.fna
1064                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1065                                                      Klebsiella_pneumoniae_CG43.fna
1066                                                   Klebsiella_pneumoniae_UHKPC07.fna
1067                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1068                                                       Klebsiella_pneumoniae_342.fna
1069                                                  Klebsiella_pneumoniae_500_1420.fna
1070                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1071                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1072                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1073                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1074                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1075                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
1076                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1077                                  Klebsiella_pneumoniae_subsp_pneumoniae_HS11286.fna
1078                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1079                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1080                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1081                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1082                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1083                                  Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH10.fna
1084                                                   Klebsiella_pneumoniae_UHKPC33.fna
1085                                                   Klebsiella_pneumoniae_UHKPC33.fna
1086                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
1087                                                   Klebsiella_pneumoniae_UHKPC07.fna
1088                                                   Klebsiella_pneumoniae_UHKPC07.fna
1089                                                   Klebsiella_pneumoniae_UHKPC33.fna
1090                                                   Klebsiella_pneumoniae_UHKPC07.fna
1091                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1092                                                   Klebsiella_pneumoniae_UHKPC07.fna
1093                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1094                                                           Klebsiella_pneumoniae.fna
1095                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1096                                                   Klebsiella_pneumoniae_UHKPC07.fna
1097                                                   Klebsiella_pneumoniae_UHKPC33.fna
1098                                                           Klebsiella_pneumoniae.fna
1099                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1100                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1101                                   Klebsiella_pneumoniae_subsp_pneumoniae_KPNIH1.fna
1102                                                           Klebsiella_pneumoniae.fna
1103                                                   Klebsiella_pneumoniae_UHKPC33.fna
1104                                                           Klebsiella_pneumoniae.fna
1105                                                           Klebsiella_pneumoniae.fna
1106                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1107                                                   Klebsiella_pneumoniae_UHKPC33.fna
1108                                     Klebsiella_pneumoniae_subsp_pneumoniae_1084.fna
1109                                                           Klebsiella_pneumoniae.fna
1110                                                           Klebsiella_pneumoniae.fna
1111                                                   Klebsiella_pneumoniae_UHKPC33.fna
1112                                                     Citrobacter_freundii_CFNIH1.fna
1113                                                            Citrobacter_freundii.fna
1114                                                            Citrobacter_freundii.fna
1115                                                            Citrobacter_freundii.fna
1116                                                            Citrobacter_freundii.fna
1117                                                     Citrobacter_freundii_CFNIH1.fna
1118                                                    Citrobacter_amalonaticus_Y19.fna
1119                                                     Citrobacter_freundii_CFNIH1.fna
1120                                                     Citrobacter_freundii_CFNIH1.fna
1121                                                     Citrobacter_freundii_CFNIH1.fna
1122                                                     Citrobacter_freundii_CFNIH1.fna
1123                                                    Citrobacter_rodentium_ICC168.fna
1124                                                    Citrobacter_rodentium_ICC168.fna
1125                                                     Citrobacter_freundii_CFNIH1.fna
1126                                                    Citrobacter_rodentium_ICC168.fna
1127                                                            Citrobacter_freundii.fna
1128                                                            Citrobacter_freundii.fna
1129                                                            Citrobacter_freundii.fna
1130                                                            Citrobacter_freundii.fna
1131                                                    Citrobacter_rodentium_ICC168.fna
1132                                                     Citrobacter_freundii_CFNIH1.fna
1133                                                    Citrobacter_rodentium_ICC168.fna
1134                                                    Citrobacter_amalonaticus_Y19.fna
1135                                                    Citrobacter_amalonaticus_Y19.fna
1136                                                    Citrobacter_amalonaticus_Y19.fna
1137                                                    Citrobacter_amalonaticus_Y19.fna
1138                                                    Citrobacter_amalonaticus_Y19.fna
1139                                                    Citrobacter_amalonaticus_Y19.fna
1140                                                    Citrobacter_rodentium_ICC168.fna
1141                                                  Enterobacter_aerogenes_EA1509E.fna
1142                                                  Enterobacter_aerogenes_EA1509E.fna
1143                                                  Enterobacter_aerogenes_EA1509E.fna
1144                                                  Enterobacter_aerogenes_EA1509E.fna
1145                                                Enterobacter_aerogenes_KCTC_2190.fna
1146                                                Enterobacter_aerogenes_KCTC_2190.fna
1147                                                Enterobacter_aerogenes_KCTC_2190.fna
1148                                                          Enterobacter_aerogenes.fna
1149                                                          Enterobacter_aerogenes.fna
1150                                                Enterobacter_aerogenes_KCTC_2190.fna
1151                                                  Enterobacter_aerogenes_EA1509E.fna
1152                                                Enterobacter_aerogenes_KCTC_2190.fna
1153                                                  Enterobacter_aerogenes_EA1509E.fna
1154                                                Enterobacter_aerogenes_KCTC_2190.fna
1155                                                Enterobacter_aerogenes_KCTC_2190.fna
1156                                                  Enterobacter_aerogenes_EA1509E.fna
1157                                                Enterobacter_aerogenes_KCTC_2190.fna
1158                                                  Enterobacter_aerogenes_EA1509E.fna
1159                                                          Enterobacter_sp_R4-368.fna
1160                                                          Enterobacter_sp_R4-368.fna
1161                                                          Enterobacter_sp_R4-368.fna
1162                                                          Enterobacter_sp_R4-368.fna
1163                                                          Enterobacter_sp_R4-368.fna
1164                                                          Enterobacter_sp_R4-368.fna
1165                                                             Enterobacter_sp_E20.fna
1166                                                          Enterobacter_sp_R4-368.fna
1167                                                             Enterobacter_sp_E20.fna
1168                                                          Enterobacter_sp_R4-368.fna
1169                                                             Enterobacter_sp_E20.fna
1170                                                             Enterobacter_sp_E20.fna
1171                                                             Enterobacter_sp_E20.fna
1172                                                          Enterobacter_sp_R4-368.fna
1173                                                          Enterobacter_sp_R4-368.fna
1174                                                    Erwinia_amylovora_ATCC_49946.fna
1175                                                    Erwinia_amylovora_ATCC_49946.fna
1176                                                      Erwinia_amylovora_CFBP1430.fna
1177                                                      Erwinia_amylovora_CFBP1430.fna
1178                                                    Erwinia_amylovora_ATCC_49946.fna
1179                                                    Erwinia_amylovora_ATCC_49946.fna
1180                                                    Erwinia_amylovora_ATCC_49946.fna
1181                                                      Erwinia_amylovora_CFBP1430.fna
1182                                                      Erwinia_amylovora_CFBP1430.fna
1183                                                      Erwinia_amylovora_CFBP1430.fna
1184                                                             Enterobacter_sp_E20.fna
1185                                                    Erwinia_amylovora_ATCC_49946.fna
1186                                                     Enterobacter_cloacae_ECNIH3.fna
1187                                                     Enterobacter_cloacae_ECNIH3.fna
1188                                                     Enterobacter_cloacae_ECNIH3.fna
1189                                                     Enterobacter_cloacae_ECNIH3.fna
1190                                                    Erwinia_amylovora_ATCC_49946.fna
1191                                                     Enterobacter_cloacae_ECNIH2.fna
1192                                                     Enterobacter_cloacae_ECNIH2.fna
1193                                                     Enterobacter_cloacae_ECNIH2.fna
1194                                                     Enterobacter_cloacae_ECNIH2.fna
1195                                                     Enterobacter_cloacae_ECNIH2.fna
1196                                                     Enterobacter_cloacae_ECNIH2.fna
1197                                                      Erwinia_amylovora_CFBP1430.fna
1198                                                      Erwinia_amylovora_CFBP1430.fna
1199                                                     Enterobacter_cloacae_ECR091.fna
1200                                                     Enterobacter_cloacae_ECR091.fna
1201                                                     Enterobacter_cloacae_EcWSU1.fna
1202                                                     Enterobacter_cloacae_EcWSU1.fna
1203                                                     Enterobacter_cloacae_ECR091.fna
1204                                                     Enterobacter_cloacae_ECR091.fna
1205                                                     Enterobacter_cloacae_ECNIH3.fna
1206                                                     Enterobacter_cloacae_ECNIH3.fna
1207                                                     Enterobacter_cloacae_ECNIH3.fna
1208                                                     Enterobacter_cloacae_ECR091.fna
1209                                                        Enterobacter_asburiae_L1.fna
1210                                                     Enterobacter_cloacae_ECNIH2.fna
1211                                                     Enterobacter_cloacae_EcWSU1.fna
1212                                                        Enterobacter_asburiae_L1.fna
1213                                                        Enterobacter_asburiae_L1.fna
1214                                                     Enterobacter_cloacae_EcWSU1.fna
1215                                                     Enterobacter_cloacae_ECNIH2.fna
1216                                                     Enterobacter_cloacae_ECNIH3.fna
1217                                                        Enterobacter_asburiae_L1.fna
1218                                                        Enterobacter_asburiae_L1.fna
1219                                                        Enterobacter_asburiae_L1.fna
1220                                                          Enterobacter_aerogenes.fna
1221                                                        Enterobacter_asburiae_L1.fna
1222                                                          Enterobacter_aerogenes.fna
1223                                                        Enterobacter_asburiae_L1.fna
1224                                                      Enterobacter_asburiae_LF7a.fna
1225                                                           Enterobacter_asburiae.fna
1226                                                           Enterobacter_asburiae.fna
1227                                                           Enterobacter_asburiae.fna
1228                                                           Enterobacter_asburiae.fna
1229                                                          Enterobacter_aerogenes.fna
1230                                                          Enterobacter_aerogenes.fna
1231                                                          Enterobacter_aerogenes.fna
1232                                                      Enterobacter_asburiae_LF7a.fna
1233                                                      Enterobacter_asburiae_LF7a.fna
1234                                                      Enterobacter_asburiae_LF7a.fna
1235                                                           Enterobacter_asburiae.fna
1236                                                     Enterobacter_cloacae_ECR091.fna
1237                                                     Enterobacter_cloacae_ECR091.fna
1238                                                      Enterobacter_asburiae_LF7a.fna
1239                                                           Enterobacter_asburiae.fna
1240                                                      Enterobacter_asburiae_LF7a.fna
1241                                                     Enterobacter_cloacae_EcWSU1.fna
1242                                                      Enterobacter_asburiae_LF7a.fna
1243                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1244                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1245                                                     Enterobacter_cloacae_EcWSU1.fna
1246                                                          Enterobacter_aerogenes.fna
1247                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1248                                                  Enterobacter_lignolyticus_SCF1.fna
1249                                                           Enterobacter_asburiae.fna
1250                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1251                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1252                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1253                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1254                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1255                                                  Enterobacter_lignolyticus_SCF1.fna
1256                                                             Enterobacter_sp_638.fna
1257                                                             Enterobacter_sp_638.fna
1258                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1259                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1260                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1261                                                             Enterobacter_sp_638.fna
1262                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1263                                       Enterobacter_cloacae_subsp_dissolvens_SDM.fna
1264                                                  Enterobacter_lignolyticus_SCF1.fna
1265                                                  Enterobacter_lignolyticus_SCF1.fna
1266                                                             Enterobacter_sp_638.fna
1267                                                             Enterobacter_sp_638.fna
1268                                                             Enterobacter_sp_638.fna
1269                                                             Enterobacter_sp_638.fna
1270                                                       Enterobacter_cloacae_P101.fna
1271                                                           Enterobacter_asburiae.fna
1272                                                     Enterobacter_cloacae_ECR091.fna
1273                                                  Enterobacter_lignolyticus_SCF1.fna
1274                                                            Enterobacter_cloacae.fna
1275                                                             Enterobacter_sp_E20.fna
1276                                                  Enterobacter_lignolyticus_SCF1.fna
1277                                                            Enterobacter_cloacae.fna
1278                                                       Enterobacter_cloacae_P101.fna
1279                                                     Enterobacter_cloacae_EcWSU1.fna
1280                                                       Enterobacter_cloacae_P101.fna
1281                                                       Enterobacter_cloacae_P101.fna
1282                                                       Enterobacter_cloacae_P101.fna
1283                                                       Enterobacter_cloacae_P101.fna
1284                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1285                                                            Enterobacter_cloacae.fna
1286                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1287                                                     Enterobacter_cloacae_EcWSU1.fna
1288                                                       Enterobacter_cloacae_P101.fna
1289                                                            Enterobacter_cloacae.fna
1290                                                            Enterobacter_cloacae.fna
1291                                                             Enterobacter_sp_E20.fna
1292                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1293                                                            Enterobacter_cloacae.fna
1294                                                            Enterobacter_cloacae.fna
1295                                                            Enterobacter_cloacae.fna
1296                                                       Enterobacter_cloacae_P101.fna
1297                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1298                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1299                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1300                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1301                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1302                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1303                                      Enterobacter_cloacae_subsp_cloacae_ENHKU01.fna
1304                                   Enterobacter_cloacae_subsp_cloacae_ATCC_13047.fna
1305                                               Cronobacter_muytjensii_ATCC_51329.fna
1306                                                  Enterobacter_lignolyticus_SCF1.fna
1307                                               Cronobacter_muytjensii_ATCC_51329.fna
1308                                               Cronobacter_muytjensii_ATCC_51329.fna
1309                                               Cronobacter_muytjensii_ATCC_51329.fna
1310                                               Cronobacter_muytjensii_ATCC_51329.fna
1311                                               Cronobacter_muytjensii_ATCC_51329.fna
1312                                               Cronobacter_muytjensii_ATCC_51329.fna

Notes

  • a bunch of Selmonella & Klebsiella




In [ ]:

Content source: nick-youngblut/SIPSim

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