mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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_000913 | 4,604,344 | 0 | C | T | 46.1% | 52.2 / 59.5 | 77 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 501,575 | 0 | A | C | 38.5% | 46.9 / 19.9 | 39 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 29,496 | 0 | T | A | 36.2% | 67.6 / 30.4 | 47 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 34.4% | 83.3 / 27.1 | 61 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.3% | 51.0 / 11.0 | 31 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 753,125 | 0 | T | A | 29.2% | 143.4 / 17.9 | 65 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 501,564 | 0 | A | C | 28.2% | 70.2 / 14.8 | 39 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.3% | 73.6 / 11.9 | 37 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 501,572 | 0 | A | C | 23.7% | 66.7 / 10.8 | 38 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 372,640 | 0 | T | G | 22.9% | 129.1 / 12.4 | 61 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.4% | 106.1 / 11.2 | 56 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,111,747 | 0 | G | T | 21.4% | 119.1 / 12.4 | 42 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.3% | 139.5 / 12.6 | 64 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 81 (1.110) | 16 (0.240) | 13/260 | 3.4 | 16.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 88 (1.290) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 51 (0.700) | 12 (0.190) | 11/246 | 3.7 | 19.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 55 (0.850) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1780767 = | 67 (0.920) | 4 (0.060) | 4/260 | 6.4 | 6.7% | coding (367/939 nt) | ydiR | putative electron transfer flavoprotein subunit YdiR |
| ? | NC_000913 | 1780852 = | 48 (0.710) | coding (452/939 nt) | ydiR | putative electron transfer flavoprotein subunit YdiR | |||||
| * | ? | NC_000913 | = 72218 | NA (NA) | 4 (0.070) | 3/226 | 6.4 | NA | noncoding (4/34 nt) | other | REP7b |
| ? | NC_000913 | = 2673777 | NA (NA) | noncoding (1/34 nt) | other | REP185 | |||||
| * | ? | NC_000913 | = 3003695 | 90 (1.240) | 4 (0.060) | 4/262 | 6.5 | 4.6% | coding (207/480 nt) | xdhC | putative xanthine dehydrogenase iron‑sulfur‑binding subunit XdhC |
| ? | NC_000913 | = 3004236 | 83 (1.210) | coding (1551/1779 nt) | ygeV | putative sigma(54)‑dependent transcriptional regulator YgeV | |||||
| * | ? | NC_000913 | 1407314 = | 78 (1.070) | 4 (0.060) | 3/258 | 7.0 | 5.0% | coding (482/1233 nt) | dgcM | diguanylate cyclase DgcM |
| ? | NC_000913 | 1407706 = | 81 (1.200) | coding (90/1233 nt) | dgcM | diguanylate cyclase DgcM | |||||
| * | ? | NC_000913 | = 4462126 | 74 (1.020) | 3 (0.040) | 3/264 | 7.1 | 4.7% | coding (535/2139 nt) | nrdD | anaerobic ribonucleoside‑triphosphate reductase |
| ? | NC_000913 | = 4462443 | 52 (0.750) | coding (218/2139 nt) | nrdD | anaerobic ribonucleoside‑triphosphate reductase | |||||
| * | ? | NC_000913 | 1466638 = | 63 (0.870) | 3 (0.040) | 3/270 | 7.2 | 3.8% | pseudogene (1247/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | = 1466859 | 91 (1.290) | pseudogene (1468/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 1466561 | 46 (0.630) | 4 (0.060) +ATTG |
3/270 | 7.2 | 7.0% | pseudogene (1170/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | 1466638 = | 63 (0.870) | pseudogene (1247/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||