mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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_000913 | 1,287,122 | 0 | T | G | 24.0% | 42.7 / 14.8 | 25 | noncoding (115/171 nt) R19R (AGG→CGG) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 1,287,123 | 0 | G | C | 24.0% | 53.1 / 14.1 | 25 | noncoding (114/171 nt) R18R (CGC→CGG) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 1,287,124 | 0 | C | A | 24.0% | 54.4 / 10.2 | 25 | noncoding (113/171 nt) R18L (CGC→CTC) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 3,642,358 | 0 | T | A | 23.3% | 78.8 / 23.2 | 43 | intergenic (+27/+22) | dtpB/rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,642,361 | 0 | T | A | 23.3% | 81.1 / 20.3 | 43 | intergenic (+30/+19) | dtpB/rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,959,515 | 0 | T | A | 23.1% | 44.1 / 11.8 | 27 | intergenic (+70/+17) | ilvC/ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| * | NC_000913 | 3,781,051 | 0 | C | G | 22.2% | 47.4 / 14.1 | 27 | intergenic (+34/‑164) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 1,004,741 | 0 | T | G | 20.8% | 44.0 / 11.6 | 24 | intergenic (+84/‑27) | ycbF/pyrD | putative periplasmic pilin chaperone/dihydro‑orotate oxidase, FMN‑linked |
| * | NC_000913 | 2,028,158 | 0 | G | C | 20.7% | 63.6 / 14.4 | 30 | intergenic (‑141/+30) | yedQ/yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| * | NC_000913 | 288,488 | 0 | C | G | 20.0% | 57.6 / 10.0 | 25 | V225V (GTG→GTC) | yagI | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 2,028,160 | 0 | G | C | 20.0% | 63.1 / 14.7 | 30 | intergenic (‑143/+28) | yedQ/yodC | putative 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 | = 4110716 | NA (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 | = 1649883 | 35 (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 | = 4623054 | 57 (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 | = 2720039 | 36 (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 | |||||