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_0009131,596,0550TG66.7% 29.0 / 18.2 24pseudogene (1933/3861 nt)yneOpseudogene, AidA homolog
*NC_000913238,5270AG46.2% 3.0 / 49.7 39I70I (ATT→ATCykfMlethality reduction protein, putative inner membrane protein
*NC_000913757,1790GT40.0% 8.2 / 13.7 15E425* (GAG→TAG) sdhAsuccinate dehydrogenase, flavoprotein subunit
*NC_0009134,296,0600CT34.9% 45.1 / 37.9 43intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*NC_0009131,196,2200CT33.3% 30.0 / 20.0 27H366H (CAC→CATicdisocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
*NC_0009131,196,2320CT33.3% 29.8 / 20.0 27T370T (ACC→ACTicdisocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
*NC_000913763,8950CG30.3% 50.9 / 26.3 33T294T (ACC→ACGsucCsuccinyl‑CoA synthetase, beta subunit
*NC_0009133,781,0510CG26.5% 52.0 / 23.0 34intergenic (+34/‑164)lldD/trmLL‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
*NC_0009132,753,9860AT21.1% 77.9 / 15.3 38intergenic (+40/+22)bamE/ratBlipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein
*NC_000913657,5310TG20.6% 67.2 / 15.7 34intergenic (+30/+24)cspE/flcconstitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
*NC_000913657,5330AT20.6% 69.5 / 12.0 34intergenic (+32/+22)cspE/flcconstitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
*NC_000913317,5660GA20.0% 85.2 / 14.6 41pseudogene (128/129 nt)ykgQpseudogene, putative dehydrogenase
*NC_000913657,5350CA20.0% 75.3 / 11.5 35intergenic (+34/+20)cspE/flcconstitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
*NC_0009133,334,7040GC20.0% 93.3 / 20.5 40intergenic (+23/‑205)ispB/sfsBoctaprenyl diphosphate synthase/malPQ operon transcriptional activator
*NC_0009133,334,7050CT20.0% 85.4 / 11.4 40intergenic (+24/‑204)ispB/sfsBoctaprenyl diphosphate synthase/malPQ operon transcriptional activator

Marginal new junction evidence (lowest skew 10 of 35 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 199954840 (1.230)8 (0.260) 6/238 3.0 16.8% intergenic (‑68/+37) dcyD/fliY D‑cysteine desulfhydrase, PLP‑dependent/cystine transporter subunit
?NC_000913 = 1999563 42 (1.380)intergenic (‑83/+22) dcyD/fliY D‑cysteine desulfhydrase, PLP‑dependent/cystine transporter subunit
* ? NC_000913 = 52182831 (0.960)6 (0.200) 6/236 3.0 18.0% coding (1413/2415 nt) ybbP putative ABC transporter permease
?NC_000913 = 521858 26 (0.860)coding (1443/2415 nt) ybbP putative ABC transporter permease
* ? NC_000913 = 278780932 (0.990)6 (0.190) 6/254 3.2 15.8% pseudogene (1413/2253 nt) ygaQ uncharacterized protein; putative enzyme
?NC_000913 3583428 = NA (NA)noncoding (1/768 nt) IS1 repeat region
* ? NC_000913 1049778 =NA (NA)6 (0.190) 6/254 3.2 15.8% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 2787809 32 (0.990)pseudogene (1413/2253 nt) ygaQ uncharacterized protein; putative enzyme
* ? NC_000913 = 291401NA (NA)6 (0.190) 6/254 3.2 15.8% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 2787809 32 (0.990)pseudogene (1413/2253 nt) ygaQ uncharacterized protein; putative enzyme
* ? NC_000913 274620 =NA (NA)5 (0.170) 5/236 3.3 NA noncoding (530/1195 nt) IS5 repeat region
?NC_000913 274663 = NA (NA)noncoding (487/1195 nt) IS5 repeat region
* ? NC_000913 3922214 =50 (1.540)5 (0.160) 5/244 3.4 9.4% coding (227/381 nt) atpI ATP synthase, membrane‑bound accessory factor
?NC_000913 3922243 = 48 (1.540)coding (198/381 nt) atpI ATP synthase, membrane‑bound accessory factor
* ? NC_000913 1359446 =26 (0.800)6 (0.190) 5/242 3.4 18.2% intergenic (‑259/+44) puuP/puuA putrescine importer/glutamate‑‑putrescine ligase
?NC_000913 1359466 = 29 (0.940)intergenic (‑279/+24) puuP/puuA putrescine importer/glutamate‑‑putrescine ligase
* ? NC_000913 = 39860833 (1.020)5 (0.160) 5/240 3.4 13.9% coding (737/1095 nt) yaiW microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein
?NC_000913 = 398612 31 (1.010)coding (741/1095 nt) yaiW microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein
* ? NC_000913 = 429751237 (1.140)4 (0.130) 4/238 3.7 10.3% coding (1855/2148 nt) fdhF formate dehydrogenase‑H, selenopolypeptide subunit
?NC_000913 = 4297530 35 (1.150)coding (1837/2148 nt) fdhF formate dehydrogenase‑H, selenopolypeptide subunit