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 1,529,203 C→A pseudogene (1302/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,218 C→T pseudogene (1317/2037 nt) rhsE → pseudogene, Rhs family
MC JC 1,978,503 Δ776 bp insB1–insA 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 4,295,641 +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_3_pae_pgi 3423761–3424533 3424533 1–773 12 [11] [11] 12 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913_3_pae_pgi 4233761 4234665 905 13 [0] [0] 28 lysC/yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi 1207790 =5 (0.120)23 (0.640) 23/246 0.6 78.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi 1209619 = 8 (0.220)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_pgi = 12078055 (0.120)32 (0.900) 30/246 0.2 83.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi = 1209602 8 (0.220)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_pgi = 12994980 (0.000)42 (1.070) 37/270 0.1 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_pae_pgi 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913_3_pae_pgi 4218568 =55 (1.500)327 (9.540) 155/236 0.0 86.4% intergenic (+155/‑28) aceA/aceK isocitrate lyase/isocitrate dehydrogenase kinase/phosphatase
?NC_000913_3_pae_pgi = 4253290 NA (NA)noncoding (130/130 nt) RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
* ? NC_000913_3_pae_pgi 4244358 =NA (NA)17 (0.450) 10/258 2.7 NA noncoding (7/126 nt) REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences
?NC_000913_3_pae_pgi 4244384 = NA (NA)noncoding (33/126 nt) REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences