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
MC JC 168,350 Δ4 bp coding (867‑870/2244 nt) fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
RA 754,103 G→T F122L (TTC→TTA)  gltA ← citrate synthase
RA 1,159,109 A→G N414S (AAC→AGC)  ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,383,685 C→A E93* (GAA→TAA)  ycjW ← LacI family putative transcriptional repressor
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,022,710 G→T G32V (GGC→GTC)  fliQ → flagellar biosynthesis protein
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,416,239 C→A T498K (ACG→AAG)  pta → phosphate acetyltransferase
RA 2,720,668 Δ1 bp coding (716/2661 nt) pka → protein lysine acetyltransferase
RA 3,560,455 +G 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 3,799,134 G→T S60* (TCG→TAG)  waaU ← lipopolysaccharide core biosynthesis
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,284,655 T→A Y83F (TAT→TTT)  actP ← acetate transporter
RA 4,287,423 G→C intergenic (‑52/‑341) acs ← / → nrfA acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
RA 4,296,381 +GC intergenic (+587/+55) 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 123033 127581 4549 39 [35] [37] 38 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 1196245 1211466 15222 40 [35] [37] 38 [icd]–[icdC] [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 3423750–3424234 3424534–3424238 5–785 38 [37] [37] 39 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12994980 (0.000)142 (1.590) 98/276 0.0 100% 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