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 169,716 Δ2,672 bp [fhuA][fhuB] [fhuA], fhuC, fhuD, [fhuB]
MC JC 257,908 Δ776 bp [crl] [crl]
RA 909,422 G→A A543V (GCC→GTC)  poxB ← pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
JC JC 911,086 IS2 (–) +5 bp intergenic (‑37/+92) poxB ← / ← hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
RA 1,159,199 G→T G444V (GGC→GTC)  ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
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 1,668,470 G→A S32L (TCG→TTG)  mlc ← glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress 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 3,534,954 G→T L305L (CTC→CTA envZ ← sensory histidine kinase in two‑component regulatory system with OmpR
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
JC JC 3,801,411 IS5 (–) +4 bp coding (586‑589/1017 nt) waaR ← lipopolysaccharide 1,2‑glucosyltransferase; UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
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
JC JC 4,175,316 IS2 (–) +5 bp intergenic (‑290/‑68) coaA ← / → thrU pantothenate kinase/tRNA‑Thr
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,287,457 C→A intergenic (‑86/‑307) 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 123034 127560 4527 54 [51] [50] 52 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 2066248–2066606 2066606 1–359 53 [51] [49] 52 [insH1] [insH1]
* * ÷ NC_000913 3423756–3424234 3424556–3424238 5–801 52 [49] [51] 54 [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)168 (1.510) 114/264 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
* ? NC_000913 4542682 =116 (1.010)65 (0.610) 52/254 1.7 38.4% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 100 (0.930)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 4542690116 (1.010)44 (0.410) 41/254 2.9 29.7% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 100 (0.930)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)