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_0009131,287,1220TG24.0% 42.7 / 14.8 25noncoding (115/171 nt)
R19R (AGG→CGG) 
rttR
tpr
rtT sRNA, processed from tyrT transcript
protamine‑like protein
*NC_0009131,287,1230GC24.0% 53.1 / 14.1 25noncoding (114/171 nt)
R18R (CGC→CGG) ‡
rttR
tpr
rtT sRNA, processed from tyrT transcript
protamine‑like protein
*NC_0009131,287,1240CA24.0% 54.4 / 10.2 25noncoding (113/171 nt)
R18L (CGC→CTC) ‡
rttR
tpr
rtT sRNA, processed from tyrT transcript
protamine‑like protein
*NC_0009133,642,3580TA23.3% 78.8 / 23.2 43intergenic (+27/+22)dtpB/rsmJdipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
*NC_0009133,642,3610TA23.3% 81.1 / 20.3 43intergenic (+30/+19)dtpB/rsmJdipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
*NC_0009133,959,5150TA23.1% 44.1 / 11.8 27intergenic (+70/+17)ilvC/ppiCketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
*NC_0009133,781,0510CG22.2% 47.4 / 14.1 27intergenic (+34/‑164)lldD/trmLL‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
*NC_0009131,004,7410TG20.8% 44.0 / 11.6 24intergenic (+84/‑27)ycbF/pyrDputative periplasmic pilin chaperone/dihydro‑orotate oxidase, FMN‑linked
*NC_0009132,028,1580GC20.7% 63.6 / 14.4 30intergenic (‑141/+30)yedQ/yodCputative membrane‑anchored diguanylate cyclase/uncharacterized protein
*NC_000913288,4880CG20.0% 57.6 / 10.0 25V225V (GTG→GTCyagICP4‑6 prophage; putative DNA‑binding transcriptional regulator
*NC_0009132,028,1600GC20.0% 63.1 / 14.7 30intergenic (‑143/+28)yedQ/yodCputative membrane‑anchored diguanylate cyclase/uncharacterized protein

Marginal new junction evidence (lowest skew 10 of 30 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 235658 =49 (1.450)7 (0.220) 7/250 2.7 14.0% coding (345/468 nt) rnhA ribonuclease HI, degrades RNA of DNA‑RNA hybrids
?NC_000913 235684 = 41 (1.310)coding (319/468 nt) rnhA ribonuclease HI, degrades RNA of DNA‑RNA hybrids
* ? NC_000913 2004132 =34 (1.010)6 (0.180) 6/262 3.1 14.3% coding (261/1407 nt) fliD flagellar filament capping protein
?NC_000913 2004173 = 39 (1.190)coding (302/1407 nt) fliD flagellar filament capping protein
* ? NC_000913 = 4110716NA (NA)5 (0.160) 5/252 3.3 NA noncoding (7/19 nt) REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 = 4110721 NA (NA)noncoding (12/19 nt) REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences
* ? NC_000913 = 164988335 (1.040)5 (0.150) 5/260 3.4 11.8% coding (90/192 nt) ydfD Qin prophage; uncharacterized protein
?NC_000913 = 1649893 41 (1.260)coding (100/192 nt) ydfD Qin prophage; uncharacterized protein
* ? NC_000913 = 462305457 (1.690)4 (0.120) 4/256 3.7 7.1% coding (1286/1332 nt) yjjJ putative protein kinase
?NC_000913 = 4623059 50 (1.560)coding (1291/1332 nt) yjjJ putative protein kinase
* ? NC_000913 4465545 =20 (0.590)4 (0.120) 4/258 3.7 16.0% coding (636/1422 nt) treB trehalose‑specific PTS enzyme: IIB and IIC component
?NC_000913 4465581 = 23 (0.710)coding (600/1422 nt) treB trehalose‑specific PTS enzyme: IIB and IIC component
* ? NC_000913 3311399 =47 (1.390)4 (0.120) 4/256 3.7 9.7% intergenic (+1/+16) psrO/rpsO novel sRNA, function unknown/30S ribosomal subunit protein S15
?NC_000913 3311478 = 30 (0.940)coding (207/270 nt) rpsO 30S ribosomal subunit protein S15
* ? NC_000913 3165820 =17 (0.500)4 (0.120) 4/258 3.7 17.7% coding (154/2259 nt) parC DNA topoisomerase IV, subunit A
?NC_000913 3165854 = 21 (0.650)coding (120/2259 nt) parC DNA topoisomerase IV, subunit A
* ? NC_000913 2779735 =23 (0.680)4 (0.120) 4/258 3.7 16.7% coding (2992/4581 nt) ypjA adhesin‑like autotransporter
?NC_000913 2779771 = 18 (0.560)coding (2956/4581 nt) ypjA adhesin‑like autotransporter
* ? NC_000913 = 272003936 (1.060)4 (0.130) 4/252 3.7 11.2% coding (87/2661 nt) pka protein lysine acetyltransferase
?NC_000913 = 2720049 30 (0.950)coding (97/2661 nt) pka protein lysine acetyltransferase