breseq  version 0.35.4  revision f352f80f4bc9
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 1,261,297 G→T D193E (GAC→GAA prs ← phosphoribosylpyrophosphate synthase
JC JC 1,351,197 IS186 (–) +6 bp :: Δ1 bp intergenic (‑158/+205) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
RA 2,019,460 G→A V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
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 2,317,667 T→G E737A (GAA→GCA)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,632,046 G→T P164T (CCG→ACG)  guaA ← GMP synthetase (glutamine aminotransferase)
RA 3,002,530 G→A G729D (GGT→GAT)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
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
JC JC 3,890,075 IS5 (–) +4 bp coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
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 3423750–3424234 3424587–3424238 5–838 15 [14] [14] 15 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3514379 3515114 736 15 [14] [13] 15 [gph]–[dam] [gph],rpe,[dam]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =22 (0.440)26 (0.590) 26/224 0.9 49.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 34 (0.770)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780522 (0.440)14 (0.320) 13/224 2.8 34.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 34 (0.770)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)33 (0.670) 30/248 0.8 100% 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