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]
JC JC 700,614 IS1 (–) +9 bp coding (973‑981/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 1,347,104 G→T C603* (TGC→TGA)  rnb ← ribonuclease II
RA 1,630,841 C→A V25F (GTT→TTT)  ydfI ← putative NAD‑dependent D‑mannonate oxidoreductase
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 2,725,672 (C)5→4 coding (75/1299 nt) 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 3,823,664 T→C V422A (GTG→GCG)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 4,186,605 A→C H419P (CAC→CCC)  rpoC → RNA polymerase, beta prime 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 2726149–2729246 2730842–2729567 322–4694 17 [15] [16] 17 [rrfG]–[rrsG] [rrfG], rrlG, gltW, [rrsG]
* * ÷ NC_000913 3423740–3424233 3424568–3424238 6–829 17 [16] [16] 17 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =44 (1.100)13 (0.370) 12/266 2.8 27.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 30 (0.840)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)51 (1.320) 49/290 0.0 100% 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