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 1,261,471 A→C I135M (ATT→ATG)  prs ← phosphoribosylpyrophosphate synthase
MC JC 1,978,503 Δ776 bp insB1–insA 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)
JC JC 2,867,796 IS1 (+) +9 bp coding (950‑958/1140 nt) nlpD ← activator of AmiC murein hydrolase activity, lipoprotein
RA 3,002,530 G→A G729D (GGT→GAT)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
JC JC 3,367,990 IS2 (–) +5 bp coding (164‑168/1128 nt) yhcG → DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
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 3423767–3424230 3424556–3424238 9–790 9 [8] [7] 10 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3514390 3515099 710 10 [8] [7] 9 [rpe]–[dam] [rpe],[dam]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1286594 =NA (NA)10 (0.290) 8/246 2.9 NA noncoding (1/72 nt) REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913 1286619 = NA (NA)noncoding (26/72 nt) REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences
* ? NC_000913 = 12994980 (0.000)47 (1.310) 39/252 0.1 100% 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 = 454269025 (0.680)14 (0.410) 13/242 1.8 28.2% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 48 (1.400)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)