breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 3,645 2 bp→AT coding (845‑846/933 nt) thrB → homoserine kinase
RA 71,170 T→C S262P (TCG→CCG)  araC → DNA‑binding transcriptional dual regulator AraC
RA 81,102 G→A S286L (TCG→TTG)  leuB ← 3‑isopropylmalate dehydrogenase
RA 98,060 G→T G325V (GGC→GTC)  murD → UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase
RA 108,958 G→T G227V (GGC→GTC)  secA → protein translocation ATPase
RA 154,182 C→T L415L (CTG→CTA htrE ← putative fimbrial usher protein HtrE
RA 156,068 A→G V45A (GTA→GCA)  yadV ← putative fimbrial chaperone YadV
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
MC JC 260,187 Δ13,768 bp IS5‑mediated proB[ykfC] 19 genes
RA 284,535 T→G A445A (GCT→GCG yagF → D‑xylonate dehydratase
RA 292,019 C→T L174L (CTA→TTA)  yagJ → protein YagJ
RA 309,381 C→T D216N (GAT→AAT)  ecpB ← putative fimbrial chaperone EcpB
RA 309,985 T→A G14G (GGA→GGT ecpB ← putative fimbrial chaperone EcpB
JC JC 362,204 IS1 (–) +9 bp coding (968‑976/1254 nt) lacY ← lactose permease
JC JC 405,538 Δ2 bp :: IS186 (–) +7 bp :: Δ1 bp coding (101‑107/810 nt) proC ← pyrroline‑5‑carboxylate reductase
RA 410,666 C→T P175S (CCT→TCT)  mak → fructokinase
RA 421,027 C→T R14R (CGC→CGT proY → putative transporter ProY
JC JC 431,304 IS1 (–) +9 bp coding (702‑710/885 nt) tsx ← nucleoside‑specific channel‑forming protein Tsx
JC JC 467,310 IS2 (–) +5 bp [ybaE] [ybaE]
RA 472,849 A→G G84G (GGA→GGG glnK → nitrogen regulatory protein PII‑2
RA 495,622 C→T T168I (ACC→ATC)  htpG → chaperone protein HtpG
RA 534,742 G→A G276D (GGT→GAT)  gcl → glyoxylate carboligase
MC JC 575,786 Δ43,077 bp IS5‑mediated [nmpC][fepE] 39 genes
RA 619,358 G→A D369N (GAT→AAT)  fepE → polysaccharide co‑polymerase family protein FepE
RA 628,998 G→A A150T (GCG→ACG)  entA → 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase
RA 630,783 G→A G297D (GGC→GAC)  cstA → pyruvate transporter CstA
RA 635,281 G→A I32I (ATC→ATT ybdM ← ParB‑like nuclease domain‑containing protein YbdM
RA 658,024 G→T intergenic (‑86/‑923) crcB ← / → tatE F(‑) channel protein/twin arginine protein translocation system ‑ TatE protein
RA 694,941 G→A L5L (CTC→CTT miaB ← isopentenyl‑adenosine A37 tRNA methylthiolase
RA 696,470 C→T noncoding (35/75 nt) glnX ← tRNA‑Gln
RA 769,388 A→T I471F (ATC→TTC)  mngB → alpha‑mannosidase
RA 780,624 C→T noncoding (71/76 nt) lysT → tRNA‑Lys
RA 822,527 C→T E405K (GAA→AAA)  clsB ← cardiolipin synthase B
RA 883,396 C→T intergenic (‑8/‑277) ybjG ← / → mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter
RA 908,169 C→T R38R (AGG→AGA ybjT ← putative NAD(P)‑binding protein YbjT
RA 1,048,787 G→A F182F (TTC→TTT gfcB ← lipoprotein GfcB
RA 1,123,823 2 bp→AG coding (231‑232/648 nt) grxB ← reduced glutaredoxin 2
RA 1,147,792 T→A S58T (TCG→ACG)  plsX → putative phosphate acyltransferase
RA 1,169,836 A→G L180P (CTG→CCG)  ldtC ← L,D‑transpeptidase LdtC
RA 1,189,980 A→G T156T (ACT→ACC phoP ← DNA‑binding transcriptional dual regulator PhoP
RA 1,194,922 G→A T10T (ACC→ACT rluE ← 23S rRNA pseudouridine(2457) synthase
RA 1,196,220 C→T H366H (CAC→CAT icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG icd → isocitrate dehydrogenase
RA 1,196,277 C→T N385N (AAC→AAT icd → isocitrate dehydrogenase
RA 1,196,280 G→C A386A (GCG→GCC icd → isocitrate dehydrogenase
RA 1,196,283 A→G K387K (AAA→AAG icd → isocitrate dehydrogenase
RA 1,196,292 C→T T390T (ACC→ACT icd → isocitrate dehydrogenase
RA 1,196,304 G→A E394E (GAG→GAA icd → isocitrate dehydrogenase
RA 1,196,316 T→A D398E (GAT→GAA icd → isocitrate dehydrogenase
RA 1,196,325 A→G K401K (AAA→AAG icd → isocitrate dehydrogenase
RA 1,253,002 C→T intergenic (+17/+83) dhaR → / ← ycgV DNA‑binding transcriptional dual regulator DhaR/putative autotransporter adhesin YcgV
RA 1,290,670 G→A W143* (TGG→TGA rssB → regulator of RpoS
MC JC 1,299,499 Δ1,199 bp insH21 insH21
RA 1,301,992 A→T N271Y (AAT→TAT)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,306,736 T→G S325A (TCC→GCC)  oppF → murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF
RA 1,308,684 T→C intergenic (‑39/‑104) clsA ← / → yciY cardiolipin synthase A/uncharacterized protein YciY
RA 1,312,434 C→T G153S (GGC→AGC)  yciB ← inner membrane protein
JC 1,322,525 Δ9 bp coding (414‑422/1563 nt) trpE ← anthranilate synthase subunit TrpE
RA 1,331,059 2 bp→AT coding (12‑13/2598 nt) topA → DNA topoisomerase 1
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
RA 1,358,859 T→C Y110C (TAT→TGT)  puuP ← putrescine:H(+) symporter PuuP
RA 1,405,758 G→A intergenic (‑7/‑221) mcaS ← / → smrA small regulatory RNA McaS/DNA endonuclease SmrA
RA 1,441,038 G→A intergenic (‑254/‑20) ydbK ← / → ydbJ putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ
RA 1,497,385 4 bp→CAA coding (530‑533/1656 nt) opgD → glucans biosynthesis protein D
JC JC 1,579,695 IS5 (+) +4 bp coding (1093‑1096/1158 nt) ydeM ← putative anaerobic sulfatase maturation enzyme YdeM
RA 1,584,092 G→A intergenic (‑133/+115) safA ← / ← ydeP two‑component system connector SafA/putative oxidoreductase YdeP
JC JC 1,590,536 IS2 (+) +5 bp intergenic (‑535/+314) ydeT ← / ← hipA fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA
RA 1,612,653 A→G M200T (ATG→ACG)  glsB ← glutaminase 2
RA 1,629,247 C→T I11I (ATC→ATT ydfZ → putative selenoprotein YdfZ
RA 1,643,679 A→T L209Q (CTG→CAG)  ydfU ← protein YdfU
RA 1,652,331 T→C intergenic (+2346/+397) ydfD → / ← ynfP lysis protein/protein YnfP
RA 1,667,460 G→A Q369* (CAG→TAG)  mlc ← DNA‑binding transcriptional repressor Mlc
RA 1,682,459 A→G K101E (AAA→GAA)  rstA → DNA‑binding transcriptional regulator RstA
RA 1,748,841 C→T R240K (AGA→AAA)  ydhT ← uncharacterized protein YdhT
RA 1,767,014 C→T G558S (GGT→AGT)  ydiJ ← putative FAD‑linked oxidoreductase YdiJ
RA 1,848,300 2 bp→TT coding (376‑377/552 nt) ydjA ← putative oxidoreductase YdjA
RA 1,849,629 T→C L265L (TTA→CTA)  sppA → protease IV, a signal peptide peptidase
RA 1,894,839 T→C L12P (CTC→CCC)  pabB → aminodeoxychorismate synthase subunit 1
MC JC 1,978,503 Δ776 bp insB5insA5 insB5, insA5
RA 2,040,433 C→A A319D (GCC→GAC)  msrP → protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP
RA 2,041,278 G→A intergenic (+160/‑97) msrQ → / → zinT membrane‑bound flavocytochrome MsrQ/metal‑binding protein ZinT
RA 2,052,885 G→A intergenic (+871/‑758) yeeJ → / → shiA inverse autotransporter adhesin/shikimate:H(+) symporter
RA 2,104,024 G→T I162I (ATC→ATA wbbK ← putative glycosyltransferase WbbK
RA 2,111,259 Δ1 bp coding (718/900 nt) rfbD ← dTDP‑4‑dehydrorhamnose reductase
RA 2,142,598 G→A L117L (CTC→CTT udk ← uridine/cytidine kinase
RA 2,155,197 G→A Q394Q (CAG→CAA mdtA → multidrug efflux pump membrane fusion protein MdtA
RA 2,173,363 Δ2 bp intergenic (‑490/+918) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
RA 2,173,448 C→T intergenic (‑575/+834) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
JC JC 2,176,844 IS4 (–) +13 bp coding (349‑361/855 nt) gatY ← tagatose‑1,6‑bisphosphate aldolase 2
RA 2,233,609 C→T Q4* (CAG→TAG)  yeiS → DUF2542 domain‑containing protein YeiS
JC JC 2,238,948 Δ1 bp :: IS186 (–) +6 bp :: Δ2 bp coding (337‑342/1521 nt) mglA ← D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit
RA 2,242,247 C→T G241R (GGG→AGG)  yeiB ← DUF418 domain‑containing protein YeiB
RA 2,247,134 A→C Y467D (TAC→GAC)  lysP ← lysine:H(+) symporter
JC 2,278,188 (AGACCAGC)1→2 coding (50/345 nt) yejG ← protein YejG
RA 2,307,733 C→T A295T (GCG→ACG)  yojI ← ABC transporter family protein/microcin J25 efflux protein
RA 2,310,878 2 bp→TT coding (656‑657/1056 nt) ftp ← FAD:protein FMN transferase
RA 2,404,402 G→A S71L (TCG→TTG)  nuoB ← NADH:quinone oxidoreductase subunit B
RA 2,446,592 C→A P294P (CCG→CCT aroC ← chorismate synthase
RA 2,485,636 Δ1 bp coding (1263/3594 nt) evgS → sensor histidine kinase EvgS
RA 2,485,638 T→A L422* (TTA→TAA)  evgS → sensor histidine kinase EvgS
RA 2,522,369 G→A P37S (CCG→TCG)  xapR ← DNA‑binding transcriptional activator XapR
RA 2,526,821 G→A V12V (GTC→GTT yfeR ← putative DNA‑binding transcriptional regulator YfeR
MC JC 2,558,699 Δ6,790 bp intZ[eutA] intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]
RA 2,587,112 C→T A461V (GCA→GTA)  narQ → sensor histidine kinase NarQ
RA 2,668,977 C→T intergenic (‑81/‑55) hcaR ← / → hcaE DNA‑binding transcriptional dual regulator HcaR/putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha
RA 2,702,363 G→A A36V (GCC→GTC)  recO ← recombination mediator protein RecO
RA 2,769,820 T→C S40P (TCA→CCA)  yfjR → putative DNA‑binding transcriptional regulator YfjR
RA 2,774,947 G→A G544S (GGT→AGT)  yfjW → uncharacterized protein YfjW
RA 2,867,311 G→T R81S (CGT→AGT)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,867,455 G→A Q33* (CAG→TAG)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,880,635 T→C L138L (TTA→TTG casD ← type I‑E CRISPR system Cascade subunit CasD
RA 2,926,772 C→A G155G (GGC→GGA ppnN → nucleotide 5'‑monophosphate nucleosidase
RA 2,936,855 T→G A424A (GCT→GCG fucI → L‑fucose isomerase
RA 2,937,210 C→T L543F (CTC→TTC)  fucI → L‑fucose isomerase
RA 2,938,548 A→T T361S (ACG→TCG)  fucK → L‑fuculokinase
RA 3,025,601 (T)5→4 coding (1251/1401 nt) xanQ → xanthine:H(+) symporter XanQ
RA 3,070,858 T→G K129N (AAA→AAC fbaA ← fructose‑bisphosphate aldolase class II
JC JC 3,136,345 IS1 (–) +9 bp coding (19‑27/1500 nt) pitB ← metal phosphate:H(+) symporter PitB
JC JC 3,206,580 IS5 (+) +4 bp coding (118‑121/912 nt) ttdA → L(+)‑tartrate dehydratase subunit alpha
RA 3,207,549 Δ1 bp coding (179/606 nt) ttdB → L(+)‑tartrate dehydratase subunit beta
RA 3,279,276 C→G F121L (TTC→TTG kbaZ → putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone
RA 3,296,481 G→A V25M (GTG→ATG)  dolP → division and outer membrane stress‑associated lipid‑binding lipoprotein
RA 3,324,965 G→T intergenic (‑54/+36) folP ← / ← ftsH dihydropteroate synthase/ATP‑dependent zinc metalloprotease FtsH
RA 3,326,537 C→A S133S (TCG→TCT ftsH ← ATP‑dependent zinc metalloprotease FtsH
RA 3,329,743 G→T D261Y (GAT→TAT)  dacB → peptidoglycan DD‑endopeptidase DacB
RA 3,388,041 T→G T50P (ACG→CCG)  aaeB ← aromatic carboxylic acid efflux pump subunit AaeB
RA 3,411,689 G→T E13* (GAA→TAA)  yhdJ → DNA adenine methyltransferase
RA 3,433,900 C→T L71L (CTA→TTA)  def → peptide deformylase
RA 3,439,485 C→T E9K (GAG→AAG)  yhdN ← DUF1992 domain‑containing protein YhdN
RA 3,441,062 G→A S205F (TCC→TTC)  rpsD ← 30S ribosomal subunit protein S4
RA 3,474,424 T→G K43N (AAA→AAC rpsL ← 30S ribosomal subunit protein S12
RA 3,486,502 C→T T128I (ACT→ATT)  crp → DNA‑binding transcriptional dual regulator CRP
RA 3,511,466 C→T V293V (GTG→GTA yhfZ ← putative DNA‑binding transcriptional regulator YhfZ
RA 3,520,507 G→A P66L (CCC→CTC)  hofQ ← DNA utilization protein HofQ
RA 3,555,047 G→C V655L (GTC→CTC)  malT → DNA‑binding transcriptional activator MalT
RA 3,560,362 G→A intergenic (+496/+260) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,647,428 C→T A377V (GCG→GTG)  gor → glutathione reductase (NADPH)
RA 3,707,947 C→A intergenic (‑242/+669) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
RA 3,719,429 G→A intergenic (‑385/‑49) yiaF ← / → yiaG DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG
RA 3,725,176 T→G E48A (GAG→GCG)  glyQ ← glycine‑‑tRNA ligase subunit alpha
RA 3,729,440 2 bp→TT noncoding (105‑106/160 nt) xylZ ← small RNA XylZ
RA 3,730,560 C→T W69* (TGG→TAG)  xylA ← xylose isomerase
RA 3,770,539 C→T V281M (GTG→ATG)  yibH ← inner membrane protein YibH
RA 3,773,173 Δ1 bp coding (893/1914 nt) mtlA → mannitol‑specific PTS enzyme IICBA component
RA 3,773,176 C→T S299F (TCT→TTT)  mtlA → mannitol‑specific PTS enzyme IICBA component
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,925,834 C→T intergenic (‑201/+178) mnmG ← / ← mioC 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG/flavoprotein MioC
RA 3,926,991 G→A L5L (CTG→TTG)  asnC ← DNA‑binding transcriptional dual regulator AsnC
RA 3,966,530 2 bp→TT coding (114‑115/1260 nt) rho → transcription termination factor Rho
RA 4,003,502 G→T P226Q (CCG→CAG)  rarD ← putative transporter RarD
JC JC 4,123,617 IS2 (–) +5 bp coding (836‑840/1026 nt) cytR ← DNA‑binding transcriptional repressor CytR
RA 4,150,418 A→G intergenic (‑153/+29) eptC ← / ← ppc phosphoethanolamine transferase EptC/phosphoenolpyruvate carboxylase
RA 4,193,996 T→G D70A (GAT→GCT)  thiE ← thiamine phosphate synthase
RA 4,217,310 A→G S68G (AGC→GGC)  aceA → isocitrate lyase
RA 4,223,638 T→C intergenic (‑10/‑190) iclR ← / → metH DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,325,644 C→T S33N (AGC→AAC)  yjdN ← PF06983 family protein YjdN
RA 4,331,890 C→T L463L (CTC→CTT proP → osmolyte:H(+) symporter ProP
RA 4,368,641 G→T intergenic (‑314/‑23) aspA ← / → fxsA aspartate ammonia‑lyase/protein FxsA
RA 4,437,890 C→T Q62* (CAG→TAG)  ytfI → protein YtfI
RA 4,473,900 C→T G52R (GGA→AGA)  bdcA ← c‑di‑GMP‑binding biofilm dispersal mediator protein
RA 4,475,493 T→C F19F (TTT→TTC yjgL → protein YjgL
RA 4,476,605 G→A S390N (AGC→AAC)  yjgL → protein YjgL
RA 4,489,016 C→T E350K (GAA→AAA)  yjgR ← DUF853 domain‑containing protein YjgR
RA 4,510,238 T→G intergenic (+445/+452) insO → / ← fecE IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit
JC JC 4,542,042 IS1 (+) +8 bp coding (6‑13/597 nt) fimE → regulator for fimA
RA 4,562,396 A→G L94L (TTG→CTG)  yjiJ ← putative transporter YjiJ
RA 4,598,984 G→A P153L (CCG→CTG)  opgB ← phosphoglycerol transferase I

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1196340 1211504 15165 14 [13] [13] 14 [icd]–mcrA [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA
* * ÷ NC_000913 3423851–3424429 3424429 1–579 14 [13] [13] 14 [rrlD] [rrlD]
* * ÷ NC_000913 4035346–4035733 4036882–4035735 3–1537 14 [12] [13] 14 [rrsA] [rrsA]