breseq  version 0.29.0  revision 8f9c342918e4
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
RA 1,352,926 C→T G235S (GGT→AGT)  sapD ← antimicrobial peptide ABC transporter ATPase
JC JC 1,755,687 IS5 (–) +4 bp intergenic (‑546/‑8) ydhZ ← / → pykF uncharacterized protein/pyruvate kinase I
JC JC 1,907,448 IS5 (–) +4 bp coding (141‑144/144 nt) yobF ← DUF2527 family heat‑induced protein
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 3,449,388 C→T E166K (GAA→AAA)  rpsC ← 30S ribosomal subunit protein S3
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 3,905,639 (A)9→8 intergenic (‑42/+92) bglF ← / ← bglG fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component/transcriptional antiterminator of the bgl operon
RA 4,161,966 C→A L66M (CTG→ATG)  yijD → DUF1422 family inner membrane protein
RA 4,187,619 C→A T757K (ACG→AAG)  rpoC → RNA polymerase, beta prime 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 3423725–3424234 3424582–3424238 5–858 27 [26] [26] 27 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =5 (0.080)40 (0.730) 36/266 0.9 88.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 6 (0.110)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078055 (0.080)43 (0.790) 37/266 0.8 89.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 6 (0.110)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related