breseq  version 0.33.1  revision 8505477f25b3
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 1,662,350 C→T P599S (CCC→TCC)  ynfF → S‑ and N‑oxide reductase, A subunit, periplasmic
RA 1,806,319 C→G intergenic (‑236/‑51) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
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 3,560,455 +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 4,187,214 A→G D622G (GAC→GGC)  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 3423753–3424234 3424556–3424238 5–804 8 [7] [7] 10 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107552 4108512 961 8 [6] [7] 9 pfkA 6‑phosphofructokinase I
* * ÷ NC_000913 4144046 4147091 3046 8 [6] [7] 9 [pflD]–[pflC] [pflD],[pflC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 225281NA (NA)8 (0.240) 8/244 2.6 NA noncoding (1511/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
?NC_000913 = 225293 NA (NA)noncoding (1523/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
* ? NC_000913 1207790 =9 (0.260)21 (0.710) 20/222 0.6 70.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 10 (0.340)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078059 (0.260)19 (0.640) 18/222 0.8 68.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 10 (0.340)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)49 (1.480) 48/246 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