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
RA 1,685,527 A→G G354G (GGT→GGC)  fumC ← fumarate hydratase (fumarase C),aerobic Class II
RA 2,145,313 C→A S683Y (TCC→TAC)  yegE → putative diguanylate cyclase
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 2,318,095 C→G L594F (TTG→TTC)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
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 3,992,624 T→G L491R (CTG→CGG)  cyaA → adenylate cyclase
RA 4,117,005 T→A D73V (GAT→GTT)  glpK ← glycerol kinase
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 1978492 1979318 827 72 [70] [70] 71 insB1–insA insB1,insA
* * ÷ NC_000913 3423837–3424525 3424525 1–689 71 [70] [70] 79 [rrlD] [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 2579071 (0.010)162 (0.970) 98/496 0.2 99.4% intergenic (+8/‑769) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 258684 = 1 (0.010)pseudogene (9/331 nt) crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
* ? NC_000913 1207790 =38 (0.220)95 (0.590) 66/480 1.1 75.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 27 (0.170)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780537 (0.220)128 (0.790) 87/480 0.4 80.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 27 (0.170)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)85 (0.500) 56/504 2.0 100% 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
* ? NC_000913 = 19785020 (0.000)62 (0.370) 53/496 2.2 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 3721045 =182 (1.060)439 (2.570) 164/510 0.0 71.0% noncoding (413/1443 nt) IS150 repeat region
?NC_000913 = 3839774 178 (1.040)coding (220/819 nt) nlpA cytoplasmic membrane lipoprotein‑28