breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,296,0600CT40.9% 33.2 / 48.0 44intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*NC_000913126,9700GC27.3% 33.5 / 14.8 22V426L (GTT→CTT) aceFpyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
*NC_0009133,360,6440GC26.1% 34.5 / 14.9 23intergenic (+28/‑532)gltD/gltFglutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
*NC_0009133,360,6450TA26.1% 31.6 / 12.6 23intergenic (+29/‑531)gltD/gltFglutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
*NC_000913124,7440T.23.3% 112.2 / 31.4 43coding (1728/2664 nt)aceEpyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
*NC_0009133,596,2230GC23.1% 50.6 / 14.7 26L61V (CTG→GTG) livHbranched‑chain amino acid ABC transporter permease
*NC_0009133,596,2280GC23.1% 52.2 / 14.3 26A59G (GCC→GGC) ‡livHbranched‑chain amino acid ABC transporter permease
*NC_0009133,596,2290CT23.1% 45.3 / 10.4 26A59T (GCC→ACC) ‡livHbranched‑chain amino acid ABC transporter permease
*NC_000913120,1581.A21.4% 62.4 / 24.0 28intergenic (+23/+20)ampE/aroPampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
*NC_0009131,642,3700CG21.1% 87.6 / 19.5 38intergenic (+303/+119)cspF/quuQQin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
*NC_0009131,642,3730CG21.1% 91.1 / 17.3 38intergenic (+306/+116)cspF/quuQQin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
*NC_000913120,1540T.20.7% 77.2 / 16.3 29intergenic (+19/+24)ampE/aroPampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter

Marginal new junction evidence (lowest skew 10 of 37 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 207852929 (0.870)7 (0.230) 7/240 2.6 19.8% intergenic (+422/+20) yeeW/yoeD CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
?NC_000913 = 2078541 30 (0.980)intergenic (+434/+8) yeeW/yoeD CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
* ? NC_000913 = 260097338 (1.140)6 (0.190) 6/246 2.9 14.1% intergenic (+25/‑228) bcp/hyfA peroxiredoxin; thiol peroxidase, thioredoxin‑dependent/hydrogenase 4, 4Fe‑4S subunit
?NC_000913 = 2600983 37 (1.180)intergenic (+35/‑218) bcp/hyfA peroxiredoxin; thiol peroxidase, thioredoxin‑dependent/hydrogenase 4, 4Fe‑4S subunit
* ? NC_000913 = 269116835 (1.050)5 (0.170) 5/236 3.1 13.6% noncoding (173/184 nt) glmY sRNA activator of glmS mRNA, glmZ processing antagonist
?NC_000913 = 2691173 32 (1.060)noncoding (168/184 nt) glmY sRNA activator of glmS mRNA, glmZ processing antagonist
* ? NC_000913 = 385284438 (1.140)5 (0.160) 5/238 3.2 12.2% intergenic (‑60/+46) ilvB/ivbL acetolactate synthase 2 large subunit/ilvB operon leader peptide
?NC_000913 = 3852855 37 (1.220)intergenic (‑71/+35) ilvB/ivbL acetolactate synthase 2 large subunit/ilvB operon leader peptide
* ? NC_000913 2543915 =52 (1.560)5 (0.160) 5/244 3.2 10.2% coding (709/792 nt) ucpA furfural resistance protein, putative short‑chain oxidoreductase
?NC_000913 2543976 = 39 (1.250)coding (648/792 nt) ucpA furfural resistance protein, putative short‑chain oxidoreductase
* ? NC_000913 = 316201NA (NA)5 (0.160) 5/242 3.2 NA noncoding (973/1255 nt) IS3 repeat region
?NC_000913 = 316220 NA (NA)noncoding (992/1255 nt) IS3 repeat region
* ? NC_000913 4530003 =42 (1.260)5 (0.160) 5/250 3.3 11.7% coding (241/1314 nt) sgcC putative PTS system EIIC permease component
?NC_000913 4530040 = 35 (1.090)coding (204/1314 nt) sgcC putative PTS system EIIC permease component
* ? NC_000913 = 3094073NA (NA)6 (0.190) 5/246 3.3 NA noncoding (108/125 nt) REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences
?NC_000913 = 3094083 NA (NA)noncoding (118/125 nt) REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences
* ? NC_000913 233792 =42 (1.260)5 (0.150) 5/254 3.3 10.8% coding (164/1359 nt) mltD putative membrane‑bound lytic murein transglycosylase D
?NC_000913 233828 = 42 (1.290)coding (128/1359 nt) mltD putative membrane‑bound lytic murein transglycosylase D
* ? NC_000913 743425 =32 (0.960)4 (0.130) 4/238 3.5 10.3% coding (599/744 nt) ybgI NIF3 family metal‑binding protein
?NC_000913 743523 = 40 (1.310)coding (697/744 nt) ybgI NIF3 family metal‑binding protein