breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 168,066 A→T K195* (AAA→TAA)  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 1,159,109 A→G N414S (AAC→AGC)  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
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
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
RA 3,799,134 G→T S60* (TCG→TAG)  waaU ← lipopolysaccharide core biosynthesis
MC JC 3,815,859 Δ82 bp [rph][rph] [rph], [rph]
RA 3,963,061 (G)5→4 coding (1169/1485 nt) gpp ← guanosine pentaphosphatase/exopolyphosphatase
MC 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 123023 127553 4531 6 [5] [2] 6 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 1612280 1612325 46 6 [5] [5] 7 yneG DUF4186 family protein
* * ÷ NC_000913 2066277–2066464 2066588–2066466 3–312 7 [5] [4] 6 [insH1] [insH1]
* * ÷ NC_000913 3423777–3424234 3424541–3424240 7–765 6 [5] [5] 6 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 315563 =NA (NA)5 (0.200) 5/220 2.7 NA noncoding (335/1255 nt) IS3 repeat region
?NC_000913 315599 = NA (NA)noncoding (371/1255 nt) IS3 repeat region
* ? NC_000913 521820 =21 (0.750)6 (0.230) 5/222 2.7 23.3% coding (1405/2415 nt) ybbP putative ABC transporter permease
?NC_000913 521868 = 20 (0.780)coding (1453/2415 nt) ybbP putative ABC transporter permease
* ? NC_000913 1207790 =0 (0.000)14 (0.580) 13/208 0.9 93.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 2 (0.080)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078050 (0.000)30 (1.240) 25/208 0.1 96.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 2 (0.080)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related