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 257,908 Δ776 bp [crl] [crl]
RA 758,983 T→A L93Q (CTG→CAG)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
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 1,934,587 T→C L6L (TTA→TTG edd ← 6‑phosphogluconate dehydratase
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 3,560,455 +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
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 4,296,381 +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 3423742–3424547 3424547 1–806 77 [76] [71] 77 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3514364 3515105 742 77 [75] [73] 79 [gph]–[dam] [gph],rpe,[dam]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 168380 =166 (0.970)158 (0.920) 111/272 0.3 48.0% coding (897/2244 nt) fhuA ferrichrome outer membrane transporter
?NC_000913 = 169386 176 (1.030)coding (1903/2244 nt) fhuA ferrichrome outer membrane transporter
* ? NC_000913 1207790 =31 (0.180)118 (0.780) 82/240 0.8 80.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 29 (0.190)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780531 (0.180)104 (0.690) 79/240 1.0 78.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 29 (0.190)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)182 (1.090) 124/264 0.1 100% 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