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
JC JC 168,640 IS2 (+) +5 bp coding (1157‑1161/2244 nt) fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
RA 909,353 G→A A566V (GCG→GTG)  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 1,158,881 C→T S338L (TCG→TTG)  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
JC JC 2,175,712 IS1 (–) +9 bp coding (602‑610/1263 nt) gatZ ← D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA 2,413,461 G→A intergenic (‑329/‑9) yfbV ← / → ackA UPF0208 family inner membrane protein/acetate kinase A and propionate kinase 2
RA 2,469,009 G→T V266F (GTT→TTT)  gtrB → CPS‑53 (KpLE1) prophage; bactoprenol glucosyl transferase
JC 2,722,123 Δ7 bp coding (2171‑2177/2661 nt) pka → protein lysine acetyltransferase
RA 3,035,437 T→C K282R (AAG→AGG)  prfB ← peptide chain release factor RF‑2
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 3,771,708 IS3 (–) +4 bp :: +TC coding (34‑37/363 nt) yibI ← DUF3302 family inner membrane protein
RA 3,798,659 (T)8→7 coding (654/1074 nt) waaU ← lipopolysaccharide core biosynthesis
MC JC 3,815,859 Δ82 bp [rph][rph] [rph], [rph]
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 123033 127562 4530 49 [45] [46] 49 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 2066281–2066630 2066630 1–350 47 [44] [46] 47 [insH1] [insH1]
* * ÷ NC_000913 3423739–3424234 3424548–3424238 5–810 50 [46] [45] 47 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =16 (0.150)92 (0.970) 72/254 0.2 88.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 9 (0.100)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780519 (0.180)54 (0.570) 45/254 1.7 80.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 9 (0.100)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related