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 371,515 G→A A93T (GCA→ACA)  mhpC → 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
MC JC 982,486 Δ4 bp coding (1440‑1443/1848 nt) ldtD → murein L,D‑transpeptidase
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
JC JC 1,806,309 IS5 (+) +4 bp intergenic (‑226/‑58) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA 1,806,319 C→T intergenic (‑236/‑51) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA 1,806,982 G→A V205I (GTC→ATC)  pfkB → 6‑phosphofructokinase II
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
MC JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta 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 2066242–2066626 2066626 1–385 43 [41] [40] 42 [insH1] [insH1]
* * ÷ NC_000913 3423760–3424552 3424552 1–793 44 [41] [41] 42 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107515 4108514 1000 42 [38] [40] 42 [pfkA] [pfkA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 120780569 (0.690)42 (0.470) 37/248 2.2 43.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 47 (0.530)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related