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 4,235,408 Δ1 bp intergenic (‑2175/‑499) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
RA 4,296,382 +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_bme_pgi 366196 366415 220 9 [8] [8] 9 [lacZ] [lacZ]
* * ÷ NC_000913_3_bme_pgi 3423772–3424234 3424556–3424239 6–785 9 [8] [8] 9 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_bme_pgi 1207790 =7 (0.210)14 (0.470) 13/248 1.4 66.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi 1209619 = 8 (0.270)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_bme_pgi = 12078057 (0.210)16 (0.540) 14/248 1.2 69.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi = 1209602 8 (0.270)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_bme_pgi = 12994980 (0.000)19 (0.580) 16/272 1.2 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_bme_pgi 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913_3_bme_pgi 2753981 =3 (0.090)31 (0.920) 28/280 0.3 66.7% intergenic (+35/+27) bamE/ratB lipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein
?NC_000913_3_bme_pgi 4502091 = 28 (0.830)intergenic (+501/+13) yjgZ/insG uncharacterized protein/IS4 transposase
* ? NC_000913_3_bme_pgi = 27539914 (0.120)25 (0.740) 23/280 0.5 59.5% intergenic (+45/+17) bamE/ratB lipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein
?NC_000913_3_bme_pgi = 4503516 30 (0.890)intergenic (‑84/‑543) insG/yjhB IS4 transposase/putative MFS transporter, membrane protein
* ? NC_000913_3_bme_pgi 4131004 =45 (1.340)89 (2.790) 69/266 0.0 70.4% coding (1170/2433 nt) metL Bifunctional aspartokinase/homoserine dehydrogenase 2
?NC_000913_3_bme_pgi = 4295543 32 (1.000)coding (1062/1314 nt) gltP glutamate/aspartate:proton symporter