breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 1,152 (C)5→6 coding (816/2463 nt) thrA → fused aspartate kinase/homoserine dehydrogenase 1
RA 9,074 C→T S279S (TCC→TCT talB → transaldolase B
RA 45,294 A→G N372S (AAC→AGC)  fixC → putative oxidoreductase FixC
RA 63,625 G→A P719L (CCC→CTC)  polB ← DNA polymerase II
RA 126,807 T→C R371R (CGT→CGC aceF → pyruvate dehydrogenase, E2 subunit
RA 136,457 (T)8→9 coding (8/867 nt) speE ← spermidine synthase
RA 137,887 A→G K269E (AAG→GAG)  cueO → cuprous oxidase/multicopper oxidase with role in copper homeostasis
RA 140,172 C→T V352I (GTT→ATT)  gcd ← quinoprotein glucose dehydrogenase
RA 150,781 (A)6→5 coding (173/1239 nt) yadC ← fimbrial tip‑adhesin YadC
RA 244,714 Δ1 bp coding (388/768 nt) yafJ → putative amidotransferase
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
RA 280,348 A→G intergenic (‑473/+37) insA‑2 ← / ← yagB IS1 protein InsA/orphan antitoxin YagB
RA 308,344 A→G V330A (GTG→GCG)  ecpC ← putative fimbrial usher protein EcpC
RA 312,523 (C)5→6 coding (255/264 nt) ykgM ← putative ribosomal protein
RA 341,200 A→G T26A (ACC→GCC)  yahJ → putative deaminase with metallo‑dependent hydrolase domain
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
RA 413,307 T→C D816G (GAC→GGC)  sbcC ← ATP dependent, structure specific DNA nuclease ‑ SbcC subunit
RA 432,609 A→G G81G (GGT→GGC yajI ← putative lipoprotein YajI
RA 437,593 A→G S181S (AGT→AGC yajO ← 1‑deoxyxylulose‑5‑phosphate synthase YajO
RA 446,852 A→G V285A (GTA→GCA)  cyoE ← heme O synthase
RA 527,577 T→C intergenic (+36/‑4) rhsD → / → ybbC protein RhsD/PF15631 family protein YbbC
RA 597,709 T→C S77S (AGT→AGC cusB → copper/silver export system membrane fusion protein
RA 640,268 G→A P172P (CCG→CCA ahpF → alkyl hydroperoxide reductase, AhpF component
RA 734,601 C→T pseudogene (382/1434 nt) ybfO → conserved protein, rhs‑like YbfO
RA 742,172 A→G Y129H (TAT→CAT)  dtpD ← dipeptide:H(+) symporter DtpD
RA 750,625 T→C T515T (ACA→ACG ybgQ ← putative fimbrial usher protein YbgQ
RA 808,482 G→T A259D (GCC→GAC)  bioA ← adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase
RA 889,923 A→G intergenic (‑104/‑166) ybjL ← / → ybjM putative transport protein YbjL/putative inner membrane protein
RA 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp
RA 955,295 A→G R446R (CGT→CGC ycaO ← ribosomal protein S12 methylthiotransferase accessory factor YcaO
RA 1,004,160 (G)7→8 coding (214/711 nt) ycbF → putative fimbrial chaperone YcbF
RA 1,005,368 C→T Q201* (CAA→TAA)  pyrD → dihydroorotate dehydrogenase, type 2
RA 1,010,898 C→T A312V (GCC→GTC)  uup → ATP‑binding protein with possible role in replication
RA 1,013,628 T→C S124P (TCT→CCT)  pqiB → intermembrane transport protein PqiB
RA 1,023,381 T→C D168G (GAC→GGC)  yccS ← putative transporter YccS
RA 1,073,232 A→G F260F (TTT→TTC rutA ← pyrimidine oxygenase
RA 1,134,819 A→G T31A (ACT→GCT)  flgG → flagellar basal‑body rod protein FlgG
RA 1,143,140 T→C T410A (ACT→GCT)  rne ← ribonuclease E
RA 1,157,814 (C)6→7 intergenic (+240/‑55) ycfH → / → ptsG putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component
RA 1,167,064 T→C V327A (GTT→GCT)  ndh → NADH:quinone oxidoreductase II
RA 1,187,117 A→G intergenic (+47/+2) pepT → / ← roxA peptidase T/ribosomal protein‑arginine oxygenase
RA 1,193,012 A→G G254G (GGT→GGC mnmA ← tRNA‑specific 2‑thiouridylase
RA 1,206,210 T→C pseudogene (80/792 nt) jayE → e14 prophage; putative protein JayE
RA 1,206,379 C→T pseudogene (249/792 nt) jayE → e14 prophage; putative protein JayE
RA 1,212,088 (C)8→9 intergenic (‑85/+172) iraM ← / ← ymgK anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK
RA 1,220,971 G→A pseudogene (1371/2648 nt) ycgH → putative transporter component, N‑terminal fragment
RA 1,258,763 A→G intergenic (‑250/‑28) pth ← / → ychH peptidyl‑tRNA hydrolase/stress‑induced protein
RA 1,289,676 A→G A144A (GCA→GCG rssA → putative patatin‑like phospholipase RssA
MC JC 1,299,499 Δ1,199 bp insH21 insH21
RA 1,303,471 T→C R191R (CGT→CGC oppB → murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB
RA 1,321,873 C→T E358E (GAG→GAA trpE ← anthranilate synthase subunit TrpE
RA 1,325,794 A→G Q350R (CAG→CGG)  yciQ → DUF2207 domain‑containing protein YciQ
JC 1,351,196 (G)7→10 intergenic (‑157/+211) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD
RA 1,371,015 T→C V267A (GTG→GCG)  ycjM → glucosylglycerate phosphorylase
RA 1,429,354 A→G A102A (GCA→GCG stfR → Rac prophage; putative membrane protein
RA 1,433,359 T→C T106A (ACC→GCC)  pinR ← Rac prophage; putative site‑specific recombinase
RA 1,541,351 C→T E414K (GAA→AAA)  narZ ← nitrate reductase Z subunit alpha
RA 1,551,142 C→A L228M (CTG→ATG)  fdnH → formate dehydrogenase N subunit beta
RA 1,596,491 A→G pseudogene (1596/5422 nt) yneO ← AIDA‑I family autotransporter YneO
RA 1,634,642 C→T G82S (GGC→AGC)  tfaQ ← Qin prophage; putative tail fiber assembly protein TfaQ
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarase C
RA 1,745,969 T→C K53K (AAA→AAG ydhQ ← adhesin‑like autotransporter YdhQ
RA 1,782,378 C→A A328A (GCC→GCA ydiS → putative oxidoreductase with FAD/NAD(P)‑binding domain
RA 1,791,142 T→C T35A (ACC→GCC)  ydiU ← UPF0061 family protein YdiU
RA 1,816,628 T→C S170G (AGC→GGC)  chbG ← chitin disaccharide deacetylase
RA 1,837,283 G→A L24L (CTG→CTA ynjC → putative ABC transporter membrane subunit YnjC
RA 1,845,694 A→G C423R (TGT→CGT)  topB ← DNA topoisomerase III
RA 1,851,894 (C)5→6 coding (8/642 nt) pncA → nicotinamidase
RA 1,873,384 A→G K448K (AAA→AAG dgcJ → putative diguanylate cyclase DgcJ
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
RA 1,883,644 A→G T153A (ACC→GCC)  yeaV → putative transporter YeaV
RA 1,893,022 A→G S72P (TCA→CCA)  yoaA ← putative 5' to 3' DNA helicase implicated in DNA repair
RA 1,900,304 T→C T428A (ACG→GCG)  yoaE ← putative inner membrane protein
RA 1,915,005 T→C H177R (CAC→CGC)  proQ ← RNA chaperone ProQ
RA 1,918,762 T→C V418A (GTA→GCA)  yebT → intermembrane transport protein YebT
RA 1,923,946 (G)6→7 coding (646/873 nt) yebZ ← putative inner membrane protein
RA 1,927,241 (C)6→7 coding (1599/2061 nt) ptrB ← oligopeptidase B
RA 1,971,513 Δ1 bp coding (1179/1662 nt) tar ← methyl‑accepting chemotaxis protein Tar
RA 1,975,369 T→C Q296R (CAG→CGG)  motB ← motility protein B
MC JC 1,978,503 Δ776 bp insB‑5insA‑5 insB‑5, insA‑5
RA 1,996,183 T→C N217S (AAC→AGC)  sdiA ← DNA‑binding transcriptional dual regulator SdiA
RA 2,025,603 (C)5→6 coding (93/816 nt) yedP → putative mannosyl‑3‑phosphoglycerate phosphatase
RA 2,052,343 (T)6→7 pseudogene (986/1053 nt) yeeL ← putative glycosyltransferase, N‑terminal fragment
RA 2,055,493 T→C Y145H (TAC→CAC)  amn → AMP nucleosidase
RA 2,134,004 A→G V550A (GTG→GCG)  wzc ← protein‑tyrosine kinase Wzc
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,183,854 T→C A221A (GCA→GCG thiD ← bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
RA 2,357,116 C→T S71S (AGC→AGT rpnE → inactive recombination‑promoting nuclease‑like protein RpnE
RA 2,376,205 T→C V205V (GTA→GTG menB ← 1,4‑dihydroxy‑2‑naphthoyl‑CoA synthase
RA 2,384,744 T→C I327V (ATT→GTT)  yfbK ← IPR002035/DUF3520 domain‑containing protein YfbK
RA 2,411,066 A→G V96A (GTT→GCT)  yfbS ← putative transporter YfbS
RA 2,430,853 G→A intergenic (‑90/+169) cvpA ← / ← dedD colicin V production protein/cell division protein DedD
RA 2,438,498 G→A T183T (ACG→ACA flk → putative flagella assembly protein
RA 2,446,579 T→C T299A (ACC→GCC)  aroC ← chorismate synthase
RA 2,464,616 T→C H131R (CAC→CGC)  mlaA ← intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA
RA 2,481,946 T→C A77A (GCA→GCG emrY ← tripartite efflux pump membrane subunit EmrY
RA 2,505,468 A→G L27P (CTG→CCG)  ypdE ← broad‑specificity exoaminopeptidase
RA 2,517,170 T→C A221A (GCA→GCG pdeA ← putative c‑di‑GMP phosphodiesterase PdeA
RA 2,527,823 T→C V293A (GTG→GCG)  yfeH → putative solute:Na(+) symporter
RA 2,532,530 T→C V41A (GTT→GCT)  cysK → O‑acetylserine sulfhydrylase A
RA 2,564,299 T→C V107A (GTC→GCC)  yffR → CPZ‑55 prophage; uncharacterized protein YffR
RA 2,571,410 G→A G114G (GGC→GGT eutE ← putative aldehyde dehydrogenase, ethanolamine utilization protein
RA 2,608,802 T→C S106P (TCA→CCA)  hyfG → hydrogenase 4 catalytic subunit HyfG
RA 2,653,842 T→C intergenic (+503/‑13) sseA → / → ryfA 3‑mercaptopyruvate sulfurtransferase/small regulatory RNA RyfA
RA 2,669,673 T→C A214A (GCT→GCC hcaE → putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha
RA 2,780,793 G→A A645V (GCC→GTC)  ypjA ← adhesin‑like autotransporter YpjA
RA 2,810,502 T→C A53A (GCT→GCC ygaH → L‑valine exporter subunit YgaH
RA 2,811,134 A→G H122R (CAC→CGC)  mprA → DNA‑binding transcriptional repressor MprA
RA 2,830,031 (T)7→6 coding (219/966 nt) gutQ → D‑arabinose 5‑phosphate isomerase GutQ
MC JC 2,857,096 Δ2,538 bp coding (4‑2541/2562 nt) mutS → DNA mismatch repair protein MutS
RA 2,949,993 (T)5→6 coding (752/1332 nt) argA → N‑acetylglutamate synthase
RA 3,068,157 T→C intergenic (‑77/+16) yggE ← / ← argO uncharacterized protein YggE/L‑arginine exporter
RA 3,073,340 (T)6→7 coding (352/1020 nt) epd ← D‑erythrose‑4‑phosphate dehydrogenase
RA 3,079,242 A→G V30A (GTA→GCA)  cmtB ← mannitol‑specific PTS enzyme IIA component CmtB
RA 3,102,340 (C)6→5 coding (513/720 nt) trmI ← tRNA m(7)G46 methyltransferase
RA 3,125,139 T→C K107K (AAA→AAG glcF ← glycolate dehydrogenase, putative iron‑sulfur subunit
RA 3,128,950 A→C T227P (ACC→CCC)  glcC → DNA‑binding transcriptional dual regulator GlcC
RA 3,173,233 T→C V31A (GTA→GCA)  ygiN → putative quinol monooxygenase YgiN
RA 3,194,156 A→G A431A (GCA→GCG yqiK → protein YqiK
RA 3,285,180 (G)5→6 coding (496/804 nt) agaC → galactosamine‑specific PTS enzyme IIC component
RA 3,299,195 C→T G74G (GGC→GGT yhbO → protein/nucleic acid deglycase 2
RA 3,325,154 T→C A594A (GCA→GCG ftsH ← ATP‑dependent zinc metalloprotease FtsH
RA 3,345,084 A→G Y123C (TAC→TGC)  rpoN → RNA polymerase, sigma 54 (sigma N) factor
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,356,124 A→G E467G (GAG→GGG)  gltB → glutamate synthase subunit GltB
RA 3,377,373 A→G G16G (GGT→GGC sspA ← stringent starvation protein A
RA 3,388,726 A→G V134A (GTT→GCT)  aaeA ← aromatic carboxylic acid efflux pump membrane fusion protein
RA 3,390,151 G→A R211H (CGC→CAC)  aaeR → LysR‑type transcriptional regulator AaeR
RA 3,391,872 G→A R53C (CGC→TGC)  tldD ← metalloprotease TldD
RA 3,422,311 T→C G329G (GGT→GGC yhdY → putative ABC transporter membrane subunit YhdY
RA 3,507,394 T→C E103G (GAG→GGG)  yhfU ← DUF2620 domain‑containing protein YhfU
RA 3,559,578 A→G E437E (GAA→GAG rtcR → DNA‑binding transcriptional activator RtcR
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,719,092 T→C intergenic (‑48/‑386) yiaF ← / → yiaG DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,846,225 A→G W315R (TGG→CGG)  uhpT ← hexose‑6‑phosphate:phosphate antiporter
RA 3,849,980 G→A L53L (CTG→TTG)  uhpB ← sensory histidine kinase UhpB
RA 3,860,630 (C)5→4 coding (348/894 nt) yidL → putative DNA‑binding transcriptional regulator YidL
RA 3,913,854 C→T W449* (TGG→TGA glmU ← fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase
RA 3,917,026 T→C Y117C (TAC→TGC)  atpD ← ATP synthase F1 complex subunit beta
RA 3,920,989 A→G A67A (GCT→GCC atpE ← ATP synthase Fo complex subunit c
RA 3,932,473 A→G A386A (GCA→GCG kup → K(+):H(+) symporter Kup
RA 3,982,684 (C)8→9 noncoding (79/87 nt) leuT → tRNA‑Leu
RA 4,068,294 A→G V328A (GTG→GCG)  yihQ ← sulfoquinovosidase
RA 4,269,672 (A)7→8 coding (259/714 nt) aphA → acid phosphatase/phosphotransferase
RA 4,279,976 A→G intergenic (+148/‑4) ghxP → / → yjcE guanine/hypoxanthine transporter GhxP/putative transporter YjcE
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,340,238 (T)5→4 coding (284/2268 nt) adiA ← arginine decarboxylase, degradative
RA 4,424,836 G→A intergenic (‑45/‑282) yjfY ← / → rpsF DUF1471 domain‑containing protein YjfY/30S ribosomal subunit protein S6
RA 4,445,549 A→G T480A (ACC→GCC)  tamB → translocation and assembly module subunit TamB
RA 4,467,176 A→G V24A (GTG→GCG)  treR ← DNA‑binding transcriptional repressor TreR
RA 4,480,758 T→C G343G (GGT→GGC yjgN → conserved inner membrane protein YjgN
RA 4,486,422 T→C F69L (TTC→CTC)  lptF → lipopolysaccharide transport system protein LptF
RA 4,543,321 A→G G69G (GGA→GGG fimA → type 1 fimbriae major subunit
RA 4,556,769 (T)9→8 coding (116/144 nt) ytiD → protein YtiD
RA 4,558,057 A→T I78N (ATC→AAC)  hypT ← DNA‑binding transcriptional dual regulator HypT
RA 4,606,094 (G)8→9 noncoding (72/87 nt) leuV ← tRNA‑Leu
RA 4,606,215 (G)8→9 noncoding (72/87 nt) leuP ← tRNA‑Leu
RA 4,609,352 A→G intergenic (+29/‑62) yjjG → / → prfC pyrimidine nucleotidase/peptide chain release factor RF3
RA 4,634,576 T→C G245G (GGA→GGG rob ← DNA‑binding transcriptional dual regulator Rob

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423768–3424234 3424525–3424238 5–758 17 [12] [12] 19 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =10 (0.160)79 (1.400) 45/244 0.1 90.4% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 8 (0.140)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780510 (0.160)49 (0.870) 37/244 0.4 85.3% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 8 (0.140)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 3363001 =100 (1.560)95 (1.500) 58/274 0.1 65.7% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 0 (0.000)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)86 (1.350) 54/276 0.1 97.7% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 2 (0.030)coding (3907/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 4542682 =47 (0.740)19 (0.320) 15/258 2.4 29.5% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542996 = 47 (0.790)intergenic (+363/‑119) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 = 454269047 (0.740)22 (0.370) 18/258 2.0 32.6% intergenic (+57/‑425) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 = 4542986 47 (0.790)intergenic (+353/‑129) fimE/fimA regulator for fimA/type 1 fimbriae major subunit