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

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 375,168 G→A 6.5% intergenic (+287/‑291) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 375,176 A→G 6.9% intergenic (+295/‑283) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,466,495 C→T 5.4% pseudogene (1104/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,466,504 A→G 5.2% pseudogene (1113/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,024,253 Δ1 bp 5.4% coding (286/624 nt) rcsA → transcriptional regulator of colanic acid capsular biosynthesis
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,304,523 G→C 5.7% intergenic (+130/+585) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,798 T→C 10.1% intergenic (+405/+310) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,316,782:1 +A 13.7% coding (606/651 nt) rcsB → response regulator in two‑component regulatory system with RcsC and YojN
RA 2,509,471 G→A 36.8% intergenic (‑45/‑159) glk ← / → yfeO glucokinase/putative ion channel protein
RA 2,976,725 Δ1 bp 7.1% coding (127/1032 nt) galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA 2,977,092 G→A 5.4% W165* (TGG→TAG)  galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
JC 2,977,234 Δ53 bp 5.6% coding (636‑688/1032 nt) galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA 3,419,437 C→A 6.1% pseudogene (331/960 nt) yhdW → pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
JC JC 3,526,449 IS5 (–) +4 bp 17.8% intergenic (‑300/‑17) nudE ← / → yrfF adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
JC JC 3,526,449 IS5 (+) +4 bp 78.6% intergenic (‑300/‑17) nudE ← / → yrfF adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
RA 3,528,108 T→G 25.6% L547R (CTG→CGG)  yrfF → putative RcsCDB‑response attenuator, inner membrane protein
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,687,585 T→C 5.4% E530G (GAG→GGG)  bcsC ← cellulose synthase subunit
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,953,535 G→T 9.4% A20S (GCG→TCG)  ilvD → dihydroxyacid dehydratase
RA 3,992,438 T→G 11.8% L429* (TTA→TGA)  cyaA → adenylate cyclase
JC 3,992,469 Δ4 bp 6.2% coding (1317‑1320/2547 nt) cyaA → adenylate cyclase
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,153,472 C→A 5.0% intergenic (‑374/+224) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 10.6% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 17.0% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 20.0% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 22.3% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 17.7% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2533701 2536448 2748 64 [63] [62] 64 ptsH–[pdxK] ptsH,ptsI,crr,[pdxK]
* * ÷ NC_000913 3423806–3424234 3424427–3424239 6–622 65 [61] [63] 65 [rrlD] [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =47 (0.340)97 (0.750) 69/484 NT 67.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 51 (0.400)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780547 (0.340)101 (0.790) 66/484 NT 68.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 51 (0.400)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)103 (0.760) 70/508 NT 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 3845531 =96 (0.700)80 (0.610) 57/496 NT 44.4% coding (1568/1767 nt) adeD cryptic adenine deaminase
?NC_000913 = 3992760 108 (0.820)coding (1608/2547 nt) cyaA adenylate cyclase