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 1,453,830 A→G intergenic (‑188/‑97) paaZ ← / → paaA oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase/ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA 1,529,180 T→C pseudogene (1279/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,185 C→T pseudogene (1284/2037 nt) rhsE → pseudogene, Rhs family
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
RA 1,712,449 A→G intergenic (+291/‑320) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA 1,823,788 C→A L92M (CTG→ATG)  cho → endonuclease of nucleotide excision repair
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 3423732–3424234 3424545–3424238 5–814 30 [29] [29] 30 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913_3_pae_pgi 4233761 4234665 905 49 [0] [1] 111 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 =17 (0.220)56 (0.820) 49/256 0.3 78.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi 1209619 = 15 (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 = 120780517 (0.220)50 (0.730) 42/256 0.6 76.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_pgi = 1209602 15 (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)68 (0.910) 53/280 0.3 100% 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 =84 (1.210)907 (13.870) 215/246 0.0 92.0% 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