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 1,166,727 G→C E215Q (GAA→CAA)  ndh → respiratory NADH dehydrogenase 2/cupric reductase
RA 1,529,175 T→C pseudogene (1274/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,180 T→C pseudogene (1279/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,185 C→T pseudogene (1284/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,203 C→A pseudogene (1302/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,218 C→T pseudogene (1317/2037 nt) rhsE → pseudogene, Rhs family
RA 1,731,621 G→T M845I (ATG→ATT lhr → putative ATP‑dependent helicase
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
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 3,316,818 C→G A237P (GCG→CCG)  nusA ← transcription termination/antitermination L factor
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 4,159,085 G→T C199F (TGT→TTT)  oxyR → oxidative and nitrosative stress transcriptional regulator
RA 4,234,667 Δ1 bp intergenic (‑1434/‑499) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
RA 4,295,641 +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_3_pae_pgi 3423708–3424234 3424561–3424238 5–854 63 [61] [60] 64 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi 1207790 =20 (0.170)77 (0.750) 60/252 1.1 81.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi 1209619 = 18 (0.180)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_pgi = 120780518 (0.160)89 (0.870) 62/252 0.9 84.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi = 1209602 18 (0.180)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_pgi = 12994980 (0.000)132 (1.180) 98/276 0.0 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_pae_pgi 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein