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 4,188,282 G→A R978H (CGT→CAT)  rpoC → RNA polymerase, beta prime subunit
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 new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_bme_pgi = 20563NA (NA)47 (0.850) 38/286 0.5 94.0% intergenic (‑55/+252) insA/rpsT IS1 repressor TnpA/30S ribosomal subunit protein S20
?NC_000913_3_bme_pgi = 61489 3 (0.050)coding (1776/2907 nt) rapA RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
* ? NC_000913_3_bme_pgi 61481 =2 (0.040)60 (1.090) 52/284 0.1 70.6% coding (1784/2907 nt) rapA RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
?NC_000913_3_bme_pgi = 1050544 48 (0.870)intergenic (+14/+419) insB1/cspH IS1 transposase B/stress protein, member of the CspA‑family
* ? NC_000913_3_bme_pgi = 275149NA (NA)59 (1.060) 36/286 0.7 96.7% intergenic (‑32/‑176) insH1/mmuP IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter
?NC_000913_3_bme_pgi = 869877 2 (0.040)coding (467/1539 nt) gsiB glutathione ABC transporter periplasmic binding protein
* ? NC_000913_3_bme_pgi 687851 =NA (NA)47 (0.850) 38/286 0.5 97.9% 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 =23 (0.420)22 (0.450) 19/254 2.2 49.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi 1209619 = 24 (0.490)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_bme_pgi = 120780523 (0.420)28 (0.570) 27/254 1.1 55.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_bme_pgi = 1209602 24 (0.490)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)63 (1.170) 52/278 0.1 100% 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