breseq  version 0.29.0  revision 8f9c342918e4
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 362,830 C→A C117F (TGT→TTT)  lacY ← lactose permease
JC JC 700,529 IS1 (+) +9 bp coding (1058‑1066/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
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 2,725,613 G→A S45L (TCA→TTA)  kgtP ← alpha‑ketoglutarate transporter
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 3,815,884 Δ2 bp pseudogene (665‑666/669 nt) rph ← ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
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 2798606 2809548 10943 74 [0] [0] 66 alaE–ygaY alaE, ygaC, ygaM, nrdH, nrdI, nrdE, nrdF, proV, proW, proX, ygaY, ygaY
* * ÷ NC_000913 3423717–3424234 3424564–3424238 5–848 31 [29] [30] 31 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12994980 (0.000)58 (0.970) 51/290 0.3 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 27986050 (0.000)74 (1.200) 58/298 0.1 100% intergenic (‑110/‑559) stpA/alaE DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
?NC_000913 3583428 = NA (NA)noncoding (1/768 nt) IS1 repeat region
* ? NC_000913 2809549 =0 (0.000)66 (1.070) 49/298 0.4 100% intergenic (+56/‑68) ygaY/ygaZ pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein/putative L‑valine exporter, norvaline resistance protein
?NC_000913 = 3584195 NA (NA)noncoding (768/768 nt) IS1 repeat region