breseq  version 0.32.0  revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 71,877 A→G 24.9% E176G (GAG→GGG)  yabI → DedA family inner membrane protein
RA 191,662 A→G 9.7% E269G (GAG→GGG)  tsf → translation elongation factor EF‑Ts
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 272,543 T→G 15.1% intergenic (+354/‑37) insN → / → eyeA pseudogene, IS911 transposase A,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/novel sRNA, function unknown, CP4‑6 propahge
RA 361,668 C→T 19.6% E65K (GAA→AAA)  lacA ← thiogalactoside acetyltransferase
RA 433,649 T→G 45.1% G65G (GGT→GGG)  ribD → fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
RA 489,597 T→G 14.2% V1021G (GTG→GGG)  mscK → mechanosensitive channel protein, intermediate conductance, K+ regulated
RA 954,374 C→G 37.3% P31P (CCG→CCC)  focA ← formate channel
RA 954,395 G→A 36.9% V24V (GTC→GTT)  focA ← formate channel
RA 1,196,305 C→T 100% R395C (CGT→TGT)  icd → isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,466,856 A→G 11.7% pseudogene (1465/2513 nt) ydbA → pseudogene, autotransporter homolog, interrupted by IS2 and IS30
JC 1,619,080 Δ35 bp 12.0% intergenic (‑172/‑6) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
RA 1,765,336 G→C 26.1% R99R (CGC→CGG)  menI ← 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase
RA 2,024,816 A→C 17.0% V3G (GTG→GGG)  dsrB ← uncharacterized protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,145,056 T→G 20.0% G597G (GGT→GGG)  yegE → putative diguanylate cyclase
RA 2,149,958 T→C 34.7% E343G (GAG→GGG)  yegI ← protein kinase‑related putative non‑specific DNA‑binding protein
RA 2,374,671 T→G 24.4% T111P (ACG→CCG)  menE ← O‑succinylbenzoate‑CoA ligase
RA 2,782,276 G→C 6.8% A150G (GCG→GGG)  ypjA ← adhesin‑like autotransporter
RA 2,796,648 A→C 19.2% V46G (GTG→GGG)  ygaU ← uncharacterized protein
RA 2,849,863 T→G 18.6% intergenic (‑16/+109) hycB ← / ← hycA hydrogenase 3, Fe‑S subunit/regulator of the transcriptional regulator FhlA
RA 2,859,421 T→C 23.8% A777A (GCT→GCC)  mutS → methyl‑directed mismatch repair protein
RA 2,874,503 T→C 17.4% G305G (GGA→GGG)  cysN ← sulfate adenylyltransferase, subunit 1
RA 3,053,513 T→C 21.4% S2G (AGC→GGC) 
*442W (TGA→TGG) 		 ubiH ←
pepP ←		 2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding
proline aminopeptidase P II
RA 3,053,524 T→C 28.3% R439G (AGA→GGA)  pepP ← proline aminopeptidase P II
RA 3,064,898 G→C 12.8% S33S (TCG→TCC)  scpC → propionyl‑CoA:succinate CoA transferase
RA 3,210,859 T→G 15.3% G27G (GGT→GGG)  rpsU → 30S ribosomal subunit protein S21
RA 3,346,883 C→T 6.0% P103L (CCG→CTG)  ptsN → sugar‑specific enzyme IIA component of PTS
RA 3,355,505 G→C 19.7% P261P (CCG→CCC)  gltB → glutamate synthase, large subunit
JC 3,525,971:1 (ATCAGG)2→3 82.1% coding (177/561 nt) nudE ← adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase
RA 3,571,895 A→G 20.2% L536P (CTC→CCC)  glgB ← 1,4‑alpha‑glucan branching enzyme
RA 3,629,381 T→C 23.2% S53G (AGC→GGC)  rbbA ← ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA 3,638,184 A→G 26.0% S182G (AGC→GGC)  pitA → phosphate transporter, low‑affinity, tellurite importer
RA 3,638,227 A→G 22.0% E196G (GAG→GGG)  pitA → phosphate transporter, low‑affinity, tellurite importer
RA 3,765,515 A→G 26.1% S1112G (AGT→GGT)  rhsA → Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor
MC JC 3,815,858 Δ82 bp 100% [rph]–[rph] [rph], [rph]
RA 3,838,901 C→T 15.7% L219L (CTG→TTG)  yicL → EamA family inner membrane putative transporter
RA 3,842,367 A→C 30.8% V12G (GTG→GGG)  yicN ← DUF1198 family protein
RA 3,951,494 T→G 16.7% pseudogene (936/984 nt) ilvG → pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted
RA 3,984,496 A→C 18.4% V504G (GTG→GGG)  aslA ← putative Ser‑type periplasmic non‑aryl sulfatase
MC JC 4,001,644 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,065,603 T→A 29.8% I55F (ATC→TTC)  yihO ← putative sulphoquinovose importer
RA 4,125,362 T→G 23.1% H483P (CAC→CCC)  priA ← Primosome factor n' (replication factor Y)
RA 4,158,652 T→G 15.6% V55G (GTG→GGG)  oxyR → oxidative and nitrosative stress transcriptional regulator
RA 4,184,542 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,213,775 G→A 18.6% F116F (TTC→TTT)  yjaB ← GNAT‑family putative N‑acetyltransferase, acetyl coenzyme A‑binding protein
RA 4,244,521 T→G 17.1% D185A (GAC→GCC)  malF ← maltose transporter subunit
RA 4,244,538 A→G 22.1% N179N (AAT→AAC)  malF ← maltose transporter subunit
RA 4,295,699 T→G 22.3% V407G (GTG→GGG)  gltP → glutamate/aspartate:proton symporter
RA 4,445,419 T→C 16.0% L436P (CTC→CCC)  tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,489,889 A→C 15.9% V59G (GTG→GGG)  yjgR ← DUF853 family protein with NTPase fold
RA 4,511,532 T→C 17.3% E295G (GAG→GGG)  fecD ← ferric citrate ABC transporter permease
RA 4,609,768 T→G 22.4% G118G (GGT→GGG)  prfC → peptide chain release factor RF‑3

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 156971 157281 311 12 [11] [11] 15 [folK] [folK]
* * ÷ NC_000913 299949 300214 266 12 [11] [11] 12 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ NC_000913 384825 385057 233 12 [11] [11] 12 yaiS/tauA putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein
* * ÷ NC_000913 583135 584248 1114 13 [11] [11] 12 [tfaX]–[appY] [tfaX], [appY]
* * ÷ NC_000913 720911 721157 247 12 [11] [11] 12 [kdpE] [kdpE]
* * ÷ NC_000913 997547 997805 259 12 [10] [11] 12 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ NC_000913 1211951 1212637 687 12 [11] [11] 12 [iraM] [iraM]
* * ÷ NC_000913 1216293 1216704 412 13 [11] [11] 12 [ymgA]–ariR [ymgA], ariR
* * ÷ NC_000913 1230387 1230584 198 12 [10] [11] 12 [hlyE] [hlyE]
* * ÷ NC_000913 1423679 1423850 172 12 [11] [11] 12 [trkG] [trkG]
* * ÷ NC_000913 1530040 1530401 362 12 [11] [11] 12 ydcD putative immunity protein for RhsE
* * ÷ NC_000913 1586545 1586756 212 12 [11] [11] 12 ydeP/ydeQ putative oxidoreductase/putative fimbrial‑like adhesin protein
* * ÷ NC_000913 1598173 1598396 224 12 [11] [11] 12 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ NC_000913 1640492 1641040 549 12 [10] [11] 12 [essQ] [essQ]
* * ÷ NC_000913 1754672 1755029 358 12 [11] [10] 12 [ydhZ] [ydhZ]
* * ÷ NC_000913 1812740 1813312 573 12 [10] [11] 12 [ydjO] [ydjO]
* * ÷ NC_000913 1907935 1908147 213 12 [10] [10] 13 yobF/yebO DUF2527 family heat‑induced protein/putative inner membrane protein
* * ÷ NC_000913 2056672 2056831 160 12 [11] [11] 13 amn/yeeN AMP nucleosidase/UPF0082 family protein
* * ÷ NC_000913 2469137 2469781 645 12 [11] [11] 12 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2470091 2470471 381 12 [11] [10] 12 [gtrS] [gtrS]
* * ÷ NC_000913 2774838 2774987 150 13 [11] [9] 12 yfjW CP4‑57 prophage, putative inner membrane protein
* * ÷ NC_000913 2786018 2786623 606 12 [11] [11] 15 [ygaQ] [ygaQ]
* * ÷ NC_000913 2995103 2995345 243 12 [9] [11] 12 [ygeN] [ygeN]
* * ÷ NC_000913 3268253 3268445 193 12 [11] [11] 12 [yhaB]–[yhaC] [yhaB], [yhaC]
* * ÷ NC_000913 3284081 3284185 105 12 [10] [9] 15 [agaB] [agaB]
* * ÷ NC_000913 3287068 3287425 358 13 [11] [11] 14 [yraH] [yraH]
* * ÷ NC_000913 3423862–3424456 3424456 1–595 12 [11] [11] 12 [rrlD] [rrlD]
* * ÷ NC_000913 3455422 3455680 259 14 [11] [11] 12 [gspC] [gspC]
* * ÷ NC_000913 3653650 3653793 144 12 [11] [10] 13 [yhiS] [yhiS]
* * ÷ NC_000913 3769618 3770072 455 12 [11] [11] 12 [yibV]–[yibU] [yibV], yibV, yibU, [yibU]
* * ÷ NC_000913 3804230 3805190 961 12 [10] [9] 12 [waaS]–[waaP] [waaS], [waaP]
* * ÷ NC_000913 4233763 4235422 1660 13 [11] [11] 12 [pgi] [pgi]
* * ÷ NC_000913 4282666 4282868 203 13 [9] [11] 12 yjcF pentapeptide repeats protein
* * ÷ NC_000913 4476743 4477165 423 13 [11] [8] 14 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4541559 4541923 365 12 [10] [11] 12 [fimB] [fimB]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)49 (0.920) 35/414 NT 100% intergenic (+9/‑768) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 458787 =2 (0.040)48 (0.910) 40/408 NT 96.1% intergenic (+87/‑101) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?NC_000913 608011 = NA (NA)intergenic (+23/‑54) hokE/insL1 toxic polypeptide, small/IS186 transposase
* ? NC_000913 = 4587990 (0.000)66 (1.260) 49/406 NT 100% intergenic (+99/‑89) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?NC_000913 = 609347 NA (NA)intergenic (+170/+112) insL1/entD IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
* ? NC_000913 700082 =76 (1.430)3 (0.060) 3/400 NT 4.1% coding (245/753 nt) umpH UMP phosphatase
?NC_000913 700110 = 66 (1.280)coding (217/753 nt) umpH UMP phosphatase
* ? NC_000913 1207790 =14 (0.260)39 (0.790) 32/382 NT 84.9% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 1 (0.020)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 120780514 (0.260)46 (0.940) 32/382 NT 86.9% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 1 (0.020)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 1293032 =2 (0.040)63 (1.180) 45/414 NT 96.9% intergenic (‑110/‑495) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
?NC_000913 = 1979270 NA (NA)intergenic (‑55/‑483) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 = 19785020 (0.000)22 (0.430) 19/398 NT 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 1979486 =0 (0.000)32 (0.600) 30/414 NT 100% intergenic (‑271/‑267) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 2101749 = NA (NA)intergenic (‑5/+146) wbbL/insH1 pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
* ? NC_000913 = 19794890 (0.000)38 (0.710) 30/414 NT 100% intergenic (‑274/‑264) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 = 2290111 NA (NA)intergenic (‑32/+1) insH1/yejO IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system