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 668,742 C→G E99Q (GAA→CAA)  rsfS ← ribosomal silencing factor
RA 1,166,727 G→C E215Q (GAA→CAA)  ndh → respiratory NADH dehydrogenase 2/cupric reductase
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
MC JC 1,978,503 Δ776 bp insB1–insA 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 2,513,351 C→A L104M (CTG→ATG)  nupC → nucleoside (except guanosine) transporter
MC JC 2,977,050 Δ46 bp coding (452‑497/1032 nt) galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
MC JC 3,397,657 Δ9 bp coding (131‑139/1470 nt) rng ← ribonuclease G
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 4,133,781 C→T intergenic (+275/‑54) metF → / → katG 5,10‑methylenetetrahydrofolate reductase/catalase‑peroxidase HPI, heme b‑containing
JC 4,233,757 +46 bp intergenic (‑524/‑583) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
JC 4,233,840 +46 bp intergenic (‑607/‑500) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
RA 4,294,815 +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_KO_pgi 366188 366429 242 46 [44] [44] 46 [lacZ]–[lacI] [lacZ],[lacI]
* * ÷ NC_000913_3_KO_pgi 1196236 1211472 15237 45 [43] [41] 45 [icd]–[icdC] [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913_3_KO_pgi 3423690–3424234 3424561–3424238 5–872 45 [44] [44] 45 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_KO_pgi = 12994980 (0.000)86 (1.010) 72/272 0.1 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_KO_pgi 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein