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
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
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
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 1196219 1211498 15280 79 [77] [77] 80 [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 3423698–3424234 3424593–3424238 5–896 79 [75] [77] 78 [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)154 (1.170) 112/272 0.0 100% 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