breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 843,749 C→A D578Y (GAT→TAT)  ybiO ← mechanosensitive channel protein, intermediate conductance
RA 1,332,633 G→T R529L (CGC→CTC)  topA → DNA topoisomerase I, omega subunit
MC JC 1,680,573 Δ814 bp [ydgI]–[folM] [ydgI], [folM]
RA 1,756,529 A→T T278S (ACC→TCC)  pykF → pyruvate kinase I
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress 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
RA 2,750,720 C→T intergenic (‑12/‑111) grpE ← / → nadK heat shock protein/NAD kinase
RA 2,810,759 G→A intergenic (+80/‑11) ygaH → / → mprA putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA 3,379,266 (C)7→6 coding (732/1128 nt) zapE ← divisome ATPase
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]
RA 4,072,171 C→A V161F (GTC→TTC)  yihT ← 6‑deoxy‑6‑sulphofructose‑1‑phosphate aldolase
RA 4,078,996 G→T intergenic (+558/‑301) yiiD → / → yiiE GNAT family putative N‑acetyltransferase/CopG family putative transcriptional regulator
RA 4,189,448 C→T Q1367* (CAG→TAG)  rpoC → RNA polymerase, beta prime subunit
MC JC 4,215,179 Δ4 bp coding (900‑903/930 nt) metA → homoserine O‑transsuccinylase
RA 4,296,381 +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 3423475–3423539 3424592–3424238 700–1118 52 [47] [49] 50 [rrfF]–[rrlD] [rrfF], thrV, rrfD, [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 2579070 (0.000)89 (1.010) 60/182 0.4 100% intergenic (+8/‑769) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 258684 = 0 (0.000)pseudogene (9/331 nt) crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
* ? NC_000913 1207790 =68 (0.710)40 (0.500) 35/166 2.2 41.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 54 (0.670)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)123 (1.340) 79/190 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