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 168,660 C→T Q393* (CAG→TAG)  fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
JC JC 911,086 IS2 (–) +5 bp intergenic (‑37/+92) poxB ← / ← hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
RA 1,159,287 C→A Y473* (TAC→TAA ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
RA 1,649,718 A→G E37G (GAA→GGA)  dicB → Qin prophage; cell division inhibition protein
RA 1,667,529 T→A K346* (AAA→TAA)  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 2,042,457 C→A G30G (GGC→GGA yodB → cytochrome b561 homolog
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
JC JC 2,415,938 IS2 (–) +5 bp coding (1192‑1196/2145 nt) pta → phosphate acetyltransferase
JC 2,721,224 (GGCTGCCG)1→2 coding (1272/2661 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 3,768,131 A→T pseudogene (911/945 nt) rhsJ → Rhs‑family protein
RA 3,964,929 C→T E234E (GAG→GAA rhlB ← ATP‑dependent RNA helicase
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 123051 127541 4491 25 [24] [23] 25 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 3423785–3424234 3424556–3424238 5–772 25 [24] [24] 25 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 609350NA (NA)28 (0.310) 25/272 2.9 36.8% noncoding (1344/1345 nt) IS186 repeat region
?NC_000913 729659 = 48 (0.530)coding (77/4194 nt) rhsC Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
* ? NC_000913 = 12994980 (0.000)95 (1.050) 74/270 0.2 100% 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 = 237583140 (0.440)30 (0.330) 26/270 2.7 42.9% coding (132/963 nt) menC O‑succinylbenzoyl‑CoA synthase
?NC_000913 2514273 = NA (NA)noncoding (1/1345 nt) IS186 repeat region