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]
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 1,434,361 IS2 (–) +5 bp intergenic (‑137/+593) ynaE ← / ← ttcC cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA 1,662,350 C→T P599S (CCC→TCC)  ynfF → S‑ and N‑oxide reductase, A subunit, periplasmic
RA 1,806,319 C→T intergenic (‑236/‑51) ydiY ← / → pfkB acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
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
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 3423755–3424234 3424530–3424239 6–776 9 [8] [7] 9 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4107529 4108511 983 11 [7] [8] 9 [pfkA] [pfkA]
* * ÷ NC_000913 4144033 4147088 3056 9 [8] [7] 9 [pflD]–[pflC] [pflD],[pflC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =37 (1.010)12 (0.370) 12/234 1.8 29.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 24 (0.750)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 3583428 =NA (NA)19 (0.520) 14/266 1.8 38.0% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 3986004 31 (0.850)coding (4/1656 nt) aslA putative Ser‑type periplasmic non‑aryl sulfatase
* ? NC_000913 = 3584195NA (NA)21 (0.570) 19/266 1.1 40.4% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 3731482 31 (0.850)coding (352/993 nt) xylF D‑xylose transporter subunit
* ? NC_000913 3721219 =37 (1.010)20 (0.550) 19/264 1.1 37.1% noncoding (587/1443 nt) IS150 repeat region
?NC_000913 3731475 = 31 (0.860)coding (345/993 nt) xylF D‑xylose transporter subunit