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 42,724 G→A A108T (GCC→ACC)  fixA → putative electron transfer flavoprotein FixA
RA 54,212 A→G V164A (GTG→GCG)  surA ← peptidyl‑prolyl cis‑trans isomerase SurA
RA 60,719 C→T G849D (GGC→GAC)  rapA ← RNA polymerase‑binding ATPase and RNAP recycling factor
RA 65,254 C→T R176H (CGC→CAC)  polB ← DNA polymerase II
RA 75,370 A→G G37G (GGT→GGC)  thiB ← thiamine ABC transporter periplasmic binding protein
RA 113,734 A→G K97K (AAA→AAG)  guaC → GMP reductase
RA 214,405 C→T R39C (CGT→TGT)  yaeQ → uncharacterized protein YaeQ
RA 235,885 T→G T40P (ACC→CCC)  rnhA ← ribonuclease HI
RA 252,574 (G)5→6 coding (274/399 nt) yafO → ribosome‑dependent mRNA interferase toxin YafO
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 268,472 A→G G163G (GGT→GGC)  ykfA ← CP4‑6 prophage; putative GTP‑binding protein YkfA
RA 271,299 C→T H233Y (CAT→TAT)  insI‑1 → IS30 transposase
RA 272,989 C→G A48G (GCC→GGC)  ykfC → CP4‑6 prophage; PF00078 domain‑containing protein YkfC
RA 273,395 A→G V183V (GTA→GTG)  ykfC → CP4‑6 prophage; PF00078 domain‑containing protein YkfC
RA 282,806 C→T R177C (CGC→TGC)  yagE → CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase
RA 367,368 A→G I48T (ATT→ACT)  lacI ← DNA‑binding transcriptional repressor LacI
RA 377,482 C→T intergenic (+171/+53) yaiL → / ← frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
RA 388,674 C→T intergenic (+28/+79) tauD → / ← hemB taurine dioxygenase/porphobilinogen synthase
RA 527,577 T→C intergenic (+36/‑4) rhsD → / → ybbC protein RhsD/PF15631 family protein YbbC
JC JC 546,661 IS1 (+) +8 bp intergenic (‑298/‑12) allD ← / → fdrA ureidoglycolate dehydrogenase/putative acyl‑CoA synthetase FdrA
RA 765,774 C→T A34A (GCG→GCA)  mngR ← DNA‑binding transcriptional repressor MngR
RA 874,787 T→G G603G (GGT→GGG)  pdeI → putative c‑di‑GMP phosphodiesterase PdeI
RA 889,923 A→G intergenic (‑104/‑166) ybjL ← / → ybjM putative transport protein YbjL/putative inner membrane protein
RA 897,067 (A)6→5 coding (934/954 nt) potH → putrescine ABC transporter membrane subunit PotH
RA 912,727 G→A P363L (CCG→CTG)  hcp ← protein S‑nitrosylase
RA 926,982 T→C T151A (ACG→GCG)  aat ← leucyl/phenylalanyl‑tRNA‑‑protein transferase
RA 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp
RA 953,523 G→A A11V (GCC→GTC)  pflB ← pyruvate formate‑lyase
RA 1,010,898 C→T A312V (GCC→GTC)  uup → ATP‑binding protein with possible role in replication
RA 1,027,676 A→G V33A (GTA→GCA)  yccT ← DUF2057 domain‑containing protein YccT
RA 1,142,142 T→C A742A (GCA→GCG)  rne ← ribonuclease E
RA 1,143,140 T→C T410A (ACT→GCT)  rne ← ribonuclease E
RA 1,174,083 G→A intergenic (‑119/+9) mfd ← / ← ycfT transcription‑repair coupling factor/inner membrane protein YcfT
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 1,212,088 (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 1,247,837 A→G S426S (AGT→AGC)  dhaM ← dihydroxyacetone kinase subunit M
RA 1,265,331 A→G D107G (GAC→GGC)  prfA → peptide chain release factor RF1
MC JC 1,299,499 Δ1,199 bp insH21 insH21
RA 1,359,720 C→T E397K (GAG→AAG)  puuA ← glutamate‑putrescine ligase
RA 1,367,155 T→A D253V (GAT→GTT)  pspF ← DNA‑binding transcriptional dual regulator PspF
RA 1,428,189 G→A H180Y (CAC→TAC)  insH‑5 ← Rac prophage; IS5 transposase and trans‑activator
RA 1,487,227 G→A intergenic (+264/‑8) hrpA → / → ydcF ATP‑dependent RNA helicase HrpA/DUF218 domain‑containing protein YdcF
RA 1,515,631 (A)5→4 coding (54/1425 nt) patD → gamma‑aminobutyraldehyde dehydrogenase
RA 1,517,532 C→T F48F (TTC→TTT)  ortT → orphan toxin OrtT
RA 1,529,416 T→G pseudogene (1527/2049 nt) rhsE → RhsE protein in rhs element
RA 1,532,018 T→C I68T (ATT→ACT)  ydcC → H repeat‑associated putative transposase YdcC
RA 1,541,351 C→T E414K (GAA→AAA)  narZ ← nitrate reductase Z subunit alpha
RA 1,555,035 C→T G212D (GGC→GAC)  maeA ← malate dehydrogenase, NAD‑requiring
RA 1,565,794 A→G G449G (GGT→GGC)  dosC ← diguanylate cyclase DosC
RA 1,576,027 A→G G531G (GGT→GGC)  yddB ← putative TonB‑dependent receptor
RA 1,634,642 C→T G82S (GGC→AGC)  tfaQ ← Qin prophage; putative tail fiber assembly protein TfaQ
RA 1,635,815 (C)5→4 coding (33/963 nt)
coding (553/570 nt)
ydfN ←
nohA ←
Qin prophage; putative side tail fiber assembly protein
Qin prophage; putative prophage DNA‑packaging protein NohA
RA 1,660,030 T→C R654R (CGT→CGC)  ynfE → putative selenate reductase YnfE
RA 1,664,747 C→T A81V (GCA→GTA)  dmsD → redox enzyme maturation protein DmsD
RA 1,671,651 A→G Q92Q (CAA→CAG)  asr → acid shock protein
RA 1,681,079 T→C V35A (GTC→GCC)  folM → dihydromonapterin reductase
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarase C
RA 1,791,033 T→C Y71C (TAC→TGC)  ydiU ← UPF0061 family protein YdiU
RA 1,802,756 (A)7→8 intergenic (‑186/‑338) thrS ← / → arpB threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment
RA 1,821,015 C→T R67H (CGC→CAC)  chbC ← N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component
RA 1,859,730 G→A A167V (GCG→GTG)  ydjK ← putative transporter YdjK
RA 1,873,384 A→G K448K (AAA→AAG)  dgcJ → putative diguanylate cyclase DgcJ
RA 1,874,137 (A)6→7 coding (46/105 nt) yoaI ← protein YoaI
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
RA 1,892,976 A→G V87A (GTC→GCC)  yoaA ← putative 5' to 3' DNA helicase implicated in DNA repair
RA 1,941,063 G→A T191T (ACC→ACT)  mepM ← peptidoglycan DD‑endopeptidase MepM
RA 1,976,679 T→C H154R (CAC→CGC)  motA ← motility protein A
MC JC 1,978,503 Δ776 bp insB‑5–insA‑5 insB‑5, insA‑5
RA 2,123,249 A→G D424D (GAT→GAC)  cpsB ← mannose‑1‑phosphate guanylyltransferase
RA 2,149,460 T→C K509R (AAG→AGG)  yegI ← protein kinase YegI
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,212,866 A→G C33R (TGT→CGT)  btsR ← DNA‑binding transcriptional activator BtsR
RA 2,296,418 T→C T203A (ACC→GCC)  ccmB ← heme trafficking system membrane protein CcmB
RA 2,302,756 T→C T86T (ACA→ACG)  napD ← NapA signal peptide‑binding chaperone NapD
RA 2,334,268 G→A pseudogene (135/4605 nt) yfaS ← putative macroglobulin family protein, N‑terminal fragment
RA 2,358,558 G→A I96I (ATC→ATT)  yfaU ← 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase
RA 2,366,570 G→A A221T (GCC→ACC)  arnB → UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase
RA 2,416,316 C→T P524S (CCG→TCG)  pta → phosphate acetyltransferase
RA 2,418,918 G→A R87C (CGC→TGC)  yfcD ← putative Nudix hydrolase
RA 2,445,459 G→A G34G (GGC→GGT)  yfcA ← conserved inner membrane protein YfcA
RA 2,446,579 T→C T299A (ACC→GCC)  aroC ← chorismate synthase
RA 2,479,086 G→A A414T (GCT→ACT)  dsdX → D‑serine transporter
RA 2,527,823 T→C V293A (GTG→GCG)  yfeH → putative solute:Na(+) symporter
RA 2,544,344 G→A R94C (CGT→TGT)  ucpA ← putative oxidoreductase
RA 2,563,254 C→T intergenic (+137/‑338) yffP → / → yffQ CPZ‑55 prophage; uncharacterized protein YffP/CPZ‑55 prophage; uncharacterized protein YffQ
RA 2,573,889 C→T A139A (GCG→GCA)  eutT ← putative ethanolamine utilization cobalamin adenosyltransferase
RA 2,594,791 T→C T357A (ACG→GCG)  tmcA ← tRNA(Met) cytidine acetyltransferase
RA 2,602,017 (C)7→8 coding (200/2019 nt) hyfB → hydrogenase 4 component B
RA 2,604,940 T→C S44P (TCA→CCA)  hyfD → hydrogenase 4 component D
RA 2,606,467 T→C V69A (GTG→GCG)  hyfE → hydrogenase 4 component E
RA 2,618,396 C→T S127S (TCG→TCA)  hda ← inibitor of reinitiation of DNA replication
RA 2,647,344 C→T L1648L (CTG→CTA)  yfhM ← alpha2‑macroglobulin
RA 2,657,197 G→A A580V (GCC→GTC)  hscA ← iron‑sulfur cluster biosynthesis chaperone HscA
RA 2,691,889 C→T A1219T (GCA→ACA)  purL ← phosphoribosylformylglycinamide synthetase
RA 2,695,843 G→A A15T (GCA→ACA)  mltF → membrane‑bound lytic murein transglycosylase F
RA 2,705,644 G→A A494V (GCG→GTG)  lepA ← elongation factor 4
RA 2,765,794 (C)7→9 intergenic (‑18/‑124) yfjM ← / → rnlA CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system
RA 2,774,081 T→C V255A (GTC→GCC)  yfjW → CP4‑57 prophage; uncharacterized protein YfjW
RA 2,777,834 C→T intergenic (+52/+312) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA
RA 2,811,134 A→G H122R (CAC→CGC)  mprA → DNA‑binding transcriptional repressor MprA
RA 2,820,897 T→C E372G (GAG→GGG)  alaS ← alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor
RA 2,824,067 C→T A94T (GCT→ACT)  pncC ← NMN aminohydrolase
RA 2,835,224 (C)5→6 coding (2202/2253 nt) hypF ← carbamoyltransferase HypF
RA 2,838,353 T→C G304G (GGA→GGG)  ascG ← DNA‑binding transcriptional repressor AscG
MC JC 2,857,096 Δ2,538 bp coding (4‑2541/2562 nt) mutS → DNA mismatch repair protein MutS
RA 2,887,921 T→C Y131C (TAC→TGC)  cysH ← phosphoadenosine phosphosulfate reductase
RA 2,910,211 A→G W159R (TGG→CGG)  mazG ← nucleoside triphosphate pyrophosphohydrolase
RA 2,949,993 (T)5→6 coding (752/1332 nt) argA → N‑acetylglutamate synthase
RA 2,988,269 T→C intergenic (+101/‑233) yqeH → / → yqeI putative LuxR family transcriptional regulator YqeH/putative transcriptional regulator YqeI
RA 2,989,323 (A)8→7 coding (20/483 nt) yqeJ → protein YqeJ
RA 3,008,407 +G coding (898/1197 nt) ygeX → 2,3‑diaminopropionate ammonia‑lyase
RA 3,011,516 C→T A19V (GCC→GTC)  yqeA → putative amino acid kinase YqeA
RA 3,031,084 T→C intergenic (‑153/‑283) ygfT ← / → uacT fused putative oxidoreductase, Fe‑S subunit and nucleotide‑binding subunit/urate:H(+) symporter
RA 3,051,343 G→A D325D (GAC→GAT)  ubiI ← 2‑octaprenylphenol hydroxylase
RA 3,058,641 (T)7→8 intergenic (‑231/+25) serA ← / ← rpiA phosphoglycerate dehydrogenase/ribose‑5‑phosphate isomerase A
RA 3,068,157 T→C intergenic (‑77/+16) yggE ← / ← argO uncharacterized protein YggE/L‑arginine exporter
RA 3,107,824 G→A G444G (GGC→GGT)  speC ← ornithine decarboxylase, biosynthetic
RA 3,120,523 T→C T253A (ACT→GCT)  glcA ← glycolate/lactate:H(+) symporter GlcA
JC 3,146,423 (TTAA)2→1 intergenic (‑162/+24) hybO ← / ← yghW hydrogenase 2 small subunit/DUF2623 domain‑containing protein YghW
RA 3,183,644 G→A intergenic (‑93/+169) yqiD ← / ← ribB protein YqiD/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA 3,216,955 T→C G59G (GGT→GGC)  nfeR → DNA‑binding transcriptional repressor NfeR
RA 3,236,458 A→G I167V (ATC→GTC)  ygjP → putative metal‑dependent hydrolase
RA 3,254,459 G→A V47V (GTG→GTA)  yhaK → bicupin‑related protein
RA 3,259,458 G→A V64V (GTC→GTT)  tdcG ← L‑serine deaminase III
RA 3,300,739 A→G I7T (ATT→ACT)  yhbS ← putative acyltransferase with acyl‑CoA N‑acyltransferase domain
RA 3,304,813 (C)7→8 coding (1005/1245 nt) mtr ← tryptophan:H(+) symporter Mtr
RA 3,305,886 T→C intergenic (‑69/+85) mtr ← / ← deaD tryptophan:H(+) symporter Mtr/ATP‑dependent RNA helicase DeaD
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,388,726 A→G V134A (GTT→GCT)  aaeA ← aromatic carboxylic acid efflux pump membrane fusion protein
RA 3,408,942 T→C Y446H (TAC→CAC)  panF → pantothenate:Na(+) symporter
RA 3,535,980 T→C D202G (GAC→GGC)  ompR ← DNA‑binding transcriptional dual regulator OmpR
RA 3,546,735 T→C G59G (GGT→GGC)  gntT → high‑affinity gluconate transporter
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,565,981 (T)7→8 coding (601/2448 nt) glgP ← glycogen phosphorylase
RA 3,705,767 A→G R8R (CGT→CGC)  dppB ← dipeptide ABC transporter membrane subunit DppB
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,845,834 A→G V445A (GTA→GCA)  uhpT ← hexose‑6‑phosphate:phosphate antiporter
RA 3,860,630 (C)5→4 coding (348/894 nt) yidL → putative DNA‑binding transcriptional regulator YidL
RA 3,875,879 G→A E148K (GAA→AAA)  yidX → putative lipoprotein YidX
RA 3,908,414 A→G intergenic (‑48/+135) pstB ← / ← pstA phosphate ABC transporter ATP binding subunit/phosphate ABC transporter membrane subunit PstA
RA 3,912,239 T→C Y477C (TAC→TGC)  glmS ← L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase
RA 3,948,805 (G)6→7 coding (1165/1521 nt) yifB ← putative magnesium chelatase YifB
RA 4,002,366 A→G N314S (AAC→AGC)  corA → Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA 4,132,127 C→T L765L (CTG→TTG)  metL → fused aspartate kinase/homoserine dehydrogenase 2
RA 4,172,011 (C)6→7 intergenic (+255/‑46) rrfB → / → murB 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase
RA 4,203,305 T→C R460R (CGT→CGC)  zraS → sensory histidine kinase ZraS
RA 4,252,853 A→G G116G (GGA→GGG)  ubiC → chorismate lyase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,445,549 A→G T480A (ACC→GCC)  tamB → translocation and assembly module subunit TamB
RA 4,461,317 A→G R448R (CGT→CGC)  nrdD ← anaerobic ribonucleoside‑triphosphate reductase
RA 4,471,590 G→A P269L (CCG→CTG)  pyrB ← aspartate carbamoyltransferase catalytic subunit
RA 4,541,335 A→G T127A (ACT→GCT)  fimB → regulator for fimA
RA 4,543,587 C→T A158V (GCG→GTG)  fimA → type 1 fimbriae major subunit
RA 4,545,520 T→C V142A (GTC→GCC)  fimD → type I fimbriae usher protein
RA 4,557,185 T→C Y65H (TAT→CAT)  iraD → anti‑adaptor protein IraD, inhibitor of sigma(S) proteolysis
RA 4,563,074 A→G V177A (GTC→GCC)  yjiK ← uncharacterized protein YjiK
RA 4,576,342 C→T pseudogene (2208/2721 nt) yjiV → putative uncharacterized protein YjiV
RA 4,580,860 (C)6→7 coding (603/1395 nt) hsdS ← type I restriction enzyme EcoKI specificity protein
RA 4,626,371 T→C L154L (TTG→CTG)  radA → DNA recombination protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1196275 1211431 15157 14 [11] [9] 14 [icd]–[icdC] [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 1432756–1433196 1433968–1433681 486–1213 14 [12] [12] 14 [tfaR]–pinR [tfaR],pinR
* * ÷ NC_000913 1528015 1529074–1528329 315–1060 13 [12] [11] 13 rhsE RhsE protein in rhs element
* * ÷ NC_000913 3423782–3424234 3426732–3424654 421–2951 13 [8] [12] 14 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3363001 =70 (1.330)88 (1.680) 58/274 0.0 71.1% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 2 (0.040)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)61 (1.150) 37/276 0.3 98.4% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 1 (0.020)coding (3907/4134 nt) rhsA rhs element protein RhsA