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 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 3,560,455 +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 4,233,746 A→G intergenic (‑513/‑2161) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
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 366255 366407 153 17 [15] [15] 17 [lacZ] [lacZ]
* * ÷ NC_000913_3_bme_pgi 3423715–3424547 3424547 1–833 17 [15] [16] 18 [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 19797 =NA (NA)44 (0.930) 39/280 0.3 95.7% intergenic (+177/+14) nhaR/insB1 transcriptional activator of nhaA/IS1 transposase B
?NC_000913_3_bme_pgi 61481 = 2 (0.040)coding (1784/2907 nt) rapA RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
* ? NC_000913_3_bme_pgi = 20563NA (NA)55 (1.160) 47/282 0.1 91.7% intergenic (‑55/+252) insA/rpsT IS1 repressor TnpA/30S ribosomal subunit protein S20
?NC_000913_3_bme_pgi = 61489 5 (0.110)coding (1776/2907 nt) rapA RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
* ? NC_000913_3_bme_pgi = 275149NA (NA)64 (1.350) 41/282 0.2 98.5% intergenic (‑32/‑176) insH1/mmuP IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter
?NC_000913_3_bme_pgi = 869877 1 (0.020)coding (467/1539 nt) gsiB glutathione ABC transporter periplasmic binding protein
* ? NC_000913_3_bme_pgi 687851 =NA (NA)30 (0.630) 23/282 1.5 96.8% intergenic (‑104/+146) gltI/insH1 glutamate/aspartate periplasmic binding protein/IS5 transposase and trans‑activator
?NC_000913_3_bme_pgi 869874 = 1 (0.020)coding (464/1539 nt) gsiB glutathione ABC transporter periplasmic binding protein
* ? NC_000913_3_bme_pgi 1207790 =7 (0.150)22 (0.520) 21/250 1.3 81.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi 1209619 = 4 (0.090)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_bme_pgi = 12078056 (0.130)40 (0.950) 36/250 0.2 89.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi = 1209602 4 (0.090)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)36 (0.780) 31/274 0.6 100% 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