breseq  version 0.27.1  revision 87c22d663cc3
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]
JC JC 573,890 IS5 (–) +4 bp intergenic (+20/‑63) ylcG → / → quuD uncharacterized protein, DLP12 prophage/DLP12 prophage; putative antitermination protein
RA 657,541 G→T intergenic (+40/+14) cspE → / ← flc constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
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 2,911,535 Δ1 bp coding (2117/2235 nt) relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase
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 3,815,810 Δ1 bp intergenic (‑42/+24) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 4,187,507 A→C N720H (AAC→CAC)  rpoC → RNA polymerase, beta prime subunit
RA 4,296,381 +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 1207790 =28 (0.160)120 (0.720) 108/566 0.5 77.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 44 (0.260)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780529 (0.160)107 (0.640) 94/566 1.1 75.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 44 (0.260)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)192 (1.110) 144/590 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