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
JC JC 153,986 IS5 (–) +4 bp coding (1438‑1441/2598 nt) htrE ← putative outer membrane usher protein
MC JC 257,908 Δ776 bp [crl] [crl]
RA 417,391 G→C A84P (GCC→CCC)  phoB → response regulator in two‑component regulatory system with PhoR
RA 702,066 G→C P229R (CCT→CGT)  nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase
RA 1,158,384 G→A W172* (TGG→TGA ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
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
RA 1,726,507 Δ1 bp coding (485/600 nt) nemR → transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
MC JC 1,978,503 Δ776 bp insB1insA 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
JC JC 2,375,828 IS186 (+) +4 bp coding (132‑135/963 nt) menC ← O‑succinylbenzoyl‑CoA synthase
RA 2,977,596 +C coding (998/1032 nt) galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
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 3,909,312 Δ774 bp [pstA][pstC] [pstA], [pstC]
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
RA 4,583,862 C→T R967H (CGT→CAT)  hsdR ← endonuclease R Type I restriction enzyme

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423759–3424234 3424530–3424239 6–772 9 [7] [8] 9 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3762361–3764072 3765195–3764080 9–2835 10 [8] [8] 9 rhsA Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
* * ÷ NC_000913 4110737 4111477 741 9 [8] [7] 9 [tpiA] [tpiA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =7 (0.240)17 (0.670) 16/252 0.6 75.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 5 (0.200)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078056 (0.210)17 (0.670) 15/252 0.7 76.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 5 (0.200)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related