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 24,855 T→C V822A (GTC→GCC)  ileS → isoleucine‑‑tRNA ligase
RA 39,897 A→G Y164H (TAC→CAC)  caiA ← crotonobetainyl‑CoA reductase
RA 136,976 C→T intergenic (‑59/‑107) yacC ← / → cueO putative lipoprotein YacC/cuprous oxidase/multicopper oxidase with role in copper homeostasis
RA 156,532 A→G S118P (TCT→CCT)  yadN ← putative fimbrial protein YadN
RA 177,992 A→G R157R (CGT→CGC btuF ← vitamin B12 ABC transporter periplasmic binding protein
RA 208,270 A→G I1049V (ATC→GTC)  dnaE → DNA polymerase III subunit alpha
RA 239,358 G→A pseudogene (169/189 nt) yafF → putative uncharacterized protein YafF
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
RA 289,143 A→G V7A (GTT→GCT)  xynR ← CP4‑6 prophage; DNA‑binding transcriptional repressor XynR
RA 312,889 A→G intergenic (‑112/+252) ykgM ← / ← ykgR putative ribosomal protein/putative membrane protein YkgR
RA 351,991 C→T D259D (GAC→GAT prpD → 2‑methylcitrate dehydratase
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
RA 424,328 A→G N604S (AAC→AGC)  malZ → maltodextrin glucosidase
RA 431,476 T→C N180D (AAC→GAC)  tsx ← nucleoside‑specific channel‑forming protein Tsx
RA 438,606 C→T S524S (TCG→TCA dxs ← 1‑deoxy‑D‑xylulose‑5‑phosphate synthase
RA 443,048 A→G intergenic (+51/+3) thiI → / ← yajL tRNA uridine 4‑sulfurtransferase/protein/nucleic acid deglycase 3
RA 493,593 T→C L501P (CTG→CCG)  dnaX → DNA polymerase III subunit tau
RA 527,577 T→C intergenic (+36/‑4) rhsD → / → ybbC protein RhsD/PF15631 family protein YbbC
RA 530,868 A→G L120P (CTG→CCG)  selU ← tRNA 2‑selenouridine synthase
RA 565,116 A→G V288A (GTC→GCC)  intD ← DLP12 prophage; putative integrase
RA 621,652 A→G L180L (TTG→CTG)  fepD ← ferric enterobactin ABC transporter membrane subunit FebD
RA 662,772 A→G F398L (TTC→CTC)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase DacA
RA 683,597 A→G G272G (GGT→GGC rihA ← pyrimidine‑specific ribonucleoside hydrolase RihA
RA 709,867 C→T D26D (GAC→GAT chiQ → lipoprotein ChiQ
RA 725,753 G→A A428A (GCC→GCT kdpB ← K(+) transporting P‑type ATPase subunit KdpB
RA 749,869 A→G G767G (GGT→GGC ybgQ ← putative fimbrial usher protein YbgQ
RA 763,438 A→G H142R (CAC→CGC)  sucC → succinyl‑CoA synthetase subunit beta
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 955,270 A→G S455P (TCG→CCG)  ycaO ← ribosomal protein S12 methylthiotransferase accessory factor YcaO
RA 1,010,898 C→T A312V (GCC→GTC)  uup → ATP‑binding protein with possible role in replication
RA 1,048,830 T→C E168G (GAG→GGG)  gfcB ← lipoprotein GfcB
RA 1,050,469 A→G K148R (AAA→AGA)  insB‑4 → IS1 protein InsB
RA 1,061,528 A→G D758G (GAC→GGC)  torA → trimethylamine N‑oxide reductase 1
RA 1,073,736 C→T G92G (GGG→GGA rutA ← pyrimidine oxygenase
RA 1,100,317 G→A A8T (GCA→ACA)  ycdZ → putative inner membrane protein
RA 1,106,515 A→G D54G (GAC→GGC)  clsC → cardiolipin synthase C
RA 1,121,290 A→G I66I (ATT→ATC dinI ← DNA damage‑inducible protein I
RA 1,122,081 A→G F176S (TTT→TCT)  pyrC ← dihydroorotase
RA 1,143,140 T→C T410A (ACT→GCT)  rne ← ribonuclease E
RA 1,144,436 A→G intergenic (‑69/‑66) rne ← / → yceQ ribonuclease E/DUF2655 domain‑containing protein YceQ
RA 1,169,369 (T)6→5 intergenic (+39/+43) bhsA → / ← ldtC DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA/L,D‑transpeptidase YcfS
RA 1,187,531 G→T A237D (GCT→GAT)  roxA ← ribosomal protein‑arginine oxygenase
RA 1,190,235 A→G V71V (GTT→GTC phoP ← DNA‑binding transcriptional dual regulator PhoP
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 1,226,800 A→G L67L (TTA→TTG ycgJ → PF05666 family protein YcgJ
RA 1,251,954 A→G T297A (ACC→GCC)  dhaR → DNA‑binding transcriptional dual regulator DhaR
RA 1,272,570 T→C S22P (TCA→CCA)  chaC → glutathione‑specific gamma‑glutamylcyclotransferase
RA 1,283,380 C→T P1173S (CCT→TCT)  narG → nitrate reductase A subunit alpha
RA 1,400,333 (A)5→6 coding (1441/1527 nt) abgT ← p‑aminobenzoyl glutamate:H(+) symporter
RA 1,403,700 A→G V289A (GTT→GCT)  abgA ← p‑aminobenzoyl‑glutamate hydrolase subunit A
RA 1,409,337 T→C P10P (CCT→CCC ynaL → protein YnaL
RA 1,509,166 T→C intergenic (‑102/‑120) yncJ ← / → hicA protein YncJ/toxin of the HicA‑HicB toxin‑antitoxin system
RA 1,527,395 A→G intergenic (+243/‑495) yncH → / → rhsE DUF5445 domain‑containing protein YncH/RhsE protein in rhs element
RA 1,531,315 A→C pseudogene (730/1054 nt) yncI → putative transposase YncI
RA 1,532,727 T→C H304H (CAT→CAC ydcC → H repeat‑associated putative transposase YdcC
RA 1,532,746 T→A W311R (TGG→AGG)  ydcC → H repeat‑associated putative transposase YdcC
RA 1,541,351 C→T E414K (GAA→AAA)  narZ ← nitrate reductase Z subunit alpha
RA 1,555,722 C→T intergenic (‑53/+104) maeA ← / ← sra malate dehydrogenase, NAD‑requiring/30S ribosomal subunit protein S22
RA 1,597,313 (C)7→8 pseudogene (774/5422 nt) yneO ← AIDA‑I family autotransporter YneO
RA 1,631,684 G→A A201V (GCA→GTA)  ydfJ ← putative transporter YdfJ
RA 1,632,949 C→T A20A (GCC→GCT ynfT → Qin prophage; protein YnfT
RA 1,634,642 C→T G82S (GGC→AGC)  tfaQ ← Qin prophage; putative tail fiber assembly protein TfaQ
RA 1,676,056 C→T G102D (GGC→GAC)  pntB ← pyridine nucleotide transhydrogenase subunit beta
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarase C
RA 1,714,326 (T)9→8 intergenic (+55/‑51) dtpA → / → gstA dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA
RA 1,721,368 A→G T35T (ACA→ACG ydhJ → putative membrane fusion protein YdhJ
RA 1,784,834 T→C D760G (GAC→GGC)  ppsA ← phosphoenolpyruvate synthetase
RA 1,803,246 G→A pseudogene (153/1900 nt) arpB → putative ankyrin repeat protein B, N‑terminal fragment
RA 1,870,782 T→C I133T (ATC→ACC)  cdgI → putative c‑di‑GMP binding protein CdgI
RA 1,870,791 T→C V136A (GTT→GCT)  cdgI → putative c‑di‑GMP binding protein CdgI
RA 1,873,384 A→G K448K (AAA→AAG dgcJ → putative diguanylate cyclase DgcJ
RA 1,874,546 (C)5→6 coding (195/447 nt) yeaL → conserved inner membrane protein YeaL
RA 1,878,801 T→C V10A (GTA→GCA)  yoaK → putative membrane protein YoaK
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
RA 1,901,041 T→C H182R (CAC→CGC)  yoaE ← putative inner membrane protein
RA 1,917,003 Δ1 bp coding (746/1284 nt) yebS → intermembrane transport protein YebS
RA 1,971,486 A→G R402R (CGT→CGC tar ← methyl‑accepting chemotaxis protein Tar
MC JC 1,978,503 Δ776 bp insB‑5insA‑5 insB‑5, insA‑5
RA 2,003,639 A→G intergenic (‑33/‑233) fliC ← / → fliD flagellar filament structural protein/flagellar filament capping protein
RA 2,016,955 (C)5→6 coding (402/1374 nt) fliI → flagellum‑specific ATP synthase FliI
RA 2,032,094 A→G L75S (TTA→TCA)  dcm ← DNA‑cytosine methyltransferase
RA 2,067,300 C→T G8R (GGA→AGA)  insH‑6 ← CP4‑44 prophage; IS5 transposase and trans‑activator
RA 2,114,296 G→A A11V (GCG→GTG)  galF ← UTP:glucose‑1‑phosphate uridylyltransferase, low activity
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,174,939 T→C P37P (CCA→CCG gatA ← galactitol‑specific PTS enzyme IIA component
RA 2,192,803 T→C intergenic (‑7/+256) yehE ← / ← mrp DUF2574 domain‑containing protein YehE/P‑loop NTPase family protein
RA 2,201,201 T→C V308A (GTC→GCC)  yehI → DUF4132 domain‑containing protein YehI
RA 2,258,987 T→C T104A (ACC→GCC)  psuK ← putative pseudouridine kinase
RA 2,280,240 T→C T82A (ACG→GCG)  rsuA ← 16S rRNA pseudouridine(516) synthase
RA 2,299,723 T→C T180A (ACG→GCG)  napG ← ferredoxin‑type protein NapG
RA 2,319,449 T→C N143S (AAC→AGC)  rcsC ← sensory histidine kinase RcsC
RA 2,370,965 T→C L20L (TTA→CTA)  arnT → lipid IVA 4‑amino‑4‑deoxy‑L‑arabinosyltransferase
RA 2,446,579 T→C T299A (ACC→GCC)  aroC ← chorismate synthase
RA 2,447,800 T→C E214G (GAA→GGA)  prmB ← 50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase
RA 2,527,823 T→C V293A (GTG→GCG)  yfeH → putative solute:Na(+) symporter
RA 2,599,252 A→G V170A (GTA→GCA)  dapA ← 4‑hydroxy‑tetrahydrodipicolinate synthase
RA 2,606,033 A→G E408G (GAG→GGG)  hyfD → hydrogenase 4 component D
RA 2,663,526 G→A V29I (GTA→ATA)  suhB → inositol‑phosphate phosphatase
RA 2,674,580 (T)7→8 coding (109/873 nt) yphB ← putative aldose 1‑epimerase YphB
RA 2,703,698 G→A G122G (GGC→GGT rnc ← RNase III
RA 2,734,543 (C)8→10 coding (492/732 nt) pgeF ← polyphenol oxidase YfiH
RA 2,767,153 G→A G57D (GGT→GAT)  rnlB → CP4‑57 prophage; antitoxin RnlB
RA 2,811,134 A→G H122R (CAC→CGC)  mprA → DNA‑binding transcriptional repressor MprA
RA 2,814,455 A→G G93G (GGT→GGC luxS ← S‑ribosylhomocysteine lyase
RA 2,853,222 T→C W363R (TGG→CGG)  hypD → Fe‑(CN)2CO cofactor assembly scaffold protein HypD
RA 2,854,143 G→A G297E (GGG→GAG)  hypE → hydrogenase maturation protein, carbamoyl dehydratase
MC JC 2,857,096 Δ2,538 bp coding (4‑2541/2562 nt) mutS → DNA mismatch repair protein MutS
RA 2,881,094 A→G L350S (TTA→TCA)  casC ← type I‑E CRISPR system Cascade subunit CasC
RA 2,949,993 (T)5→6 coding (752/1332 nt) argA → N‑acetylglutamate synthase
RA 2,973,764 T→C L33L (CTA→CTG lplT ← lysophospholipid transporter
RA 2,977,087 T→C G163G (GGT→GGC galR → DNA‑binding transcriptional dual regulator GalR
RA 2,980,423 T→C L71L (TTA→TTG ygeA ← amino acid racemase
RA 3,068,157 T→C intergenic (‑77/+16) yggE ← / ← argO uncharacterized protein YggE/L‑arginine exporter
RA 3,091,562 T→C G143G (GGT→GGC rsmE → 16S rRNA m(3)U1498 methyltransferase
RA 3,144,785 T→C N119S (AAC→AGC)  hybA ← hydrogenase 2 iron‑sulfur protein
RA 3,196,669 T→C T29A (ACC→GCC)  rfaE ← fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase
RA 3,229,464 A→G T193A (ACC→GCC)  ygjK → glycoside hydrolase
RA 3,270,481 T→C noncoding (112/377 nt) rnpB ← RNase P catalytic RNA component
RA 3,290,285 A→G D491G (GAC→GGC)  yraJ → putative fimbrial usher protein YraJ
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,366,694 T→C T9A (ACA→GCA)  insH‑10 ← IS5 transposase and trans‑activator
RA 3,385,829 G→A intergenic (+28/+28) yhcN → / ← yhcO DUF1471 domain‑containing stress‑induced protein YhcN/putative barnase inhibitor
RA 3,388,726 A→G V134A (GTT→GCT)  aaeA ← aromatic carboxylic acid efflux pump membrane fusion protein
RA 3,392,785 G→A T1158T (ACC→ACT yhdP ← AsmA2 domain‑containing protein
RA 3,548,840 G→A Q411* (CAG→TAG)  malQ ← 4‑alpha‑glucanotransferase
RA 3,559,459 T→C L398L (TTG→CTG)  rtcR → DNA‑binding transcriptional activator RtcR
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,638,124 T→C V161V (GTT→GTC pitA → metal phosphate:H(+) symporter PitA
RA 3,646,029 T→C G215G (GGT→GGC rlmJ → 23S rRNA m(6)A2030 methyltransferase
RA 3,709,561 (C)6→5 coding (915/1692 nt) eptB ← Kdo2‑lipid A phosphoethanolamine 7''‑transferase
RA 3,760,846 G→A A135V (GCG→GTG)  selA ← selenocysteine synthase
RA 3,765,305 A→G R1041R (AGA→AGG rhsA → rhs element protein RhsA
RA 3,765,307 C→G T1042S (ACC→AGC)  rhsA → rhs element protein RhsA
RA 3,803,350 G→A S263L (TCA→TTA)  waaB ← UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase
RA 3,806,651 T→C K139K (AAA→AAG waaG ← lipopolysaccharide glucosyltransferase I
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,820,592 (C)6→7 coding (579/1683 nt) ligB ← DNA ligase B
RA 3,843,478 (C)5→4 coding (312/1335 nt) adeQ ← adenine transporter
RA 3,860,630 (C)5→4 coding (348/894 nt) yidL → putative DNA‑binding transcriptional regulator YidL
RA 3,954,748 T→C V424A (GTG→GCG)  ilvD → dihydroxy‑acid dehydratase
RA 3,982,684 (C)8→9 noncoding (79/87 nt) leuT → tRNA‑Leu
RA 4,017,388 G→A G19D (GGC→GAC)  rmuC → putative recombination limiting protein RmuC
RA 4,101,899 A→G V70V (GTA→GTG kdgT → 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
RA 4,112,221 T→C intergenic (‑7/‑94) yiiQ ← / → yiiR DUF1454 domain‑containing protein YiiQ/DUF805 domain‑containing protein YiiR
RA 4,145,150 A→G T386A (ACC→GCC)  pflD → putative formate acetyltransferase 2
RA 4,286,402 C→T G324S (GGT→AGT)  acs ← acetyl‑CoA synthetase (AMP‑forming)
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,306,202 A→G D132D (GAT→GAC yjcS ← alkyl sulfatase
RA 4,310,124 A→G V286A (GTC→GCC)  alsA ← D‑allose ABC transporter ATP binding subunit
RA 4,356,143 A→G V90A (GTG→GCG)  dtpC ← dipeptide/tripeptide:H(+) symporter DtpC
JC 4,357,864 (TCA)4→3 coding (752‑754/2148 nt) cadA ← lysine decarboxylase 1
RA 4,385,931 (A)7→6 coding (228/315 nt) yjeO → conserved inner membrane protein YjeO
RA 4,445,549 A→G T480A (ACC→GCC)  tamB → translocation and assembly module subunit TamB
RA 4,458,745 (G)5→4 coding (787/1353 nt) pmbA → metalloprotease PmbA
RA 4,510,483 T→C intergenic (+350/+207) yjhV → / ← fecE KpLE2 phage‑like element; putative uncharacterized protein YjhV/ferric citrate ABC transporter ATP binding subunit
RA 4,606,215 (G)8→9 noncoding (72/87 nt) leuP ← tRNA‑Leu
RA 4,615,987 A→G V360A (GTC→GCC)  yjjI ← DUF3029 domain‑containing protein YjjI

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1433778–1434070 1434220–1434074 5–443 24 [23] [21] 24 [ynaE] [ynaE]
* * ÷ NC_000913 3423785–3424234 3424523–3424238 5–739 26 [20] [13] 26 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =5 (0.060)109 (1.430) 61/244 0.1 91.8% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 15 (0.200)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12078055 (0.060)47 (0.620) 38/244 0.7 82.9% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 15 (0.200)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)94 (1.120) 58/268 0.2 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 3363001 =122 (1.410)120 (1.400) 59/274 0.2 65.9% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 3 (0.040)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)114 (1.320) 70/276 0.1 96.6% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 4 (0.050)coding (3907/4134 nt) rhsA rhs element protein RhsA