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 124,241 C→T Q409* (CAG→TAG)  aceE → pyruvate dehydrogenase E1 component
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
JC 757,230 Δ9 bp coding (1324‑1332/1767 nt) sdhA → succinate:quinone oxidoreductase, FAD binding protein
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
MC JC 1,978,503 Δ776 bp insB‑5insA‑5 insB‑5, insA‑5
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA‑5 ← / → uspC IS1 protein InsA/universal stress protein C
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative colanic acid biosynthesis glycosyl transferase
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,662,095 C→T A13T (GCA→ACA)  iscR ← DNA‑binding transcriptional dual regulator IscR
RA 3,041,393 G→T W27C (TGG→TGT ygfZ → folate‑binding protein
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
JC 3,815,859 Δ82 bp [rph] [rph]
MC JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase subunit beta
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2066212–2066464 2066667–2066466 3–456 133 [132] [130] 135 [insH‑6] [insH‑6]
* * ÷ NC_000913 3423692–3424585 3424585 1–894 134 [132] [130] 136 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 566777 =NA (NA)10991 (44.290) 195/184 0.0 98.0% noncoding (1/1258 nt) IS3 repeat region
?NC_000913 = 572471 233 (0.930)coding (6/456 nt) ybcN DLP12 prophage; DNA base‑flipping protein
* ? NC_000913 1207790 =19 (0.080)153 (0.740) 96/154 0.4 87.5% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 28 (0.130)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780518 (0.070)189 (0.910) 100/154 0.2 89.8% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 28 (0.130)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)239 (1.000) 123/178 0.1 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein