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
RA 222,965 (A)8→7 coding (133/576 nt) gmhB → D,D‑heptose 1,7‑bisphosphate phosphatase
MC JC 257,908 Δ776 bp [crl] [crl]
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,019,460 G→A V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
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 2,904,212 G→A intergenic (+838/+535) ygcE → / ← queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
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]
JC JC 3,890,075 IS5 (–) +4 bp coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,362,665 A→C intergenic (‑39/+68) pheU ← / ← yjdC tRNA‑Phe/putative transcriptional regulator
RA 4,406,129 T→C intergenic (+144/‑61) purA → / → nsrR adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon
JC JC 4,640,551 IS1 (–) +9 bp intergenic (+9/‑383) yjjY → / → yjtD uncharacterized protein/putative methyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 772981 774213 1233 39 [38] [38] 41 [cydA]–[cydX] [cydA],cydB,[cydX]
* * ÷ NC_000913 1037673 1039320 1648 39 [38] [38] 39 cbdA–[cbdB] cbdA,[cbdB]
* * ÷ NC_000913 1166055 1167422 1368 39 [37] [38] 39 ndh ndh
* * ÷ NC_000913 3423711–3424234 3424551–3424238 5–841 39 [38] [38] 40 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =11 (0.120)47 (0.580) 35/264 2.1 81.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 11 (0.140)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780511 (0.120)75 (0.930) 59/264 0.4 87.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 11 (0.140)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)139 (1.570) 101/288 0.0 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein