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 1,685,527 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
JC JC 2,494,426 IS5 (–) +4 bp intergenic (‑24/‑269) yfdX ← / → ypdI uncharacterized protein/putative lipoprotein involved in colanic acid biosynthesis
RA 2,535,948 G→C D39H (GAT→CAT)  crr → glucose‑specific enzyme IIA component of PTS
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 4,115,901 G→A A441V (GCA→GTA)  glpK ← glycerol kinase
RA 4,268,657 C→A intergenic (+350/+152) tyrB → / ← yjbS tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
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 583070 583780 711 85 [83] [81] 84 [tfaX]–[appY] [tfaX],[appY]
* * ÷ NC_000913 1978497 1979284 788 84 [83] [82] 85 insB1–insA insB1,insA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =23 (0.120)148 (0.820) 94/480 0.3 86.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 23 (0.130)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780523 (0.120)176 (0.980) 96/480 0.3 88.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 23 (0.130)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)121 (0.640) 75/504 1.2 100% 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)77 (0.420) 56/496 2.5 100% 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 =273 (1.430)425 (2.230) 160/510 0.0 66.3% noncoding (413/1443 nt) IS150 repeat region
?NC_000913 = 3839774 160 (0.840)coding (220/819 nt) nlpA cytoplasmic membrane lipoprotein‑28