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 | 51.7% | 33.0 / 120.7 | 89 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 650,809 | 0 | T | G | 34.4% | 101.1 / 19.6 | 64 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.0% | 172.4 / 19.5 | 97 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.6% | 141.6 / 25.6 | 76 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,745,397 | 0 | A | C | 30.2% | 93.6 / 11.8 | 54 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 4,101,507 | 0 | T | G | 30.0% | 141.5 / 10.9 | 71 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,943,488 | 0 | T | G | 28.3% | 77.3 / 10.0 | 46 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 770,897 | 0 | T | G | 27.5% | 135.1 / 10.1 | 70 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| * | NC_000913 | 501,575 | 0 | A | C | 26.8% | 82.0 / 11.2 | 41 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 179.7 / 19.5 | 76 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.6% | 114.3 / 18.5 | 57 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,491,098 | 0 | A | C | 22.9% | 183.9 / 14.2 | 83 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,645,034 | 0 | A | C | 22.7% | 144.3 / 10.4 | 67 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 3,926,366 | 0 | A | C | 22.6% | 253.6 / 21.9 | 106 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 4,101,525 | 0 | C | T | 21.6% | 174.8 / 12.2 | 74 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 366,526 | 0 | T | G | 21.1% | 122.8 / 14.2 | 52 | T329P (ACC→CCC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 4,098,155 | 0 | A | C | 20.6% | 199.8 / 12.2 | 92 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,111,747 | 0 | G | T | 20.4% | 149.3 / 12.7 | 54 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,740,909 | 0 | T | G | 20.2% | 181.0 / 18.1 | 79 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| 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 | 107 (1.110) | 24 (0.270) | 22/260 | 2.5 | 18.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 108 (1.190) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 78 (0.810) | 15 (0.180) | 12/246 | 4.2 | 16.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 89 (1.040) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 95 (0.980) | 14 (0.150) | 12/260 | 4.4 | 12.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 108 (1.190) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979397 = | 93 (0.970) | 10 (0.100) | 6/276 | 6.7 | 9.7% | intergenic (‑182/‑356) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 120934 = | 103 (1.060) | 4 (0.040) | 4/262 | 7.4 | 4.0% | coding (618/1374 nt) | aroP | aromatic amino acid:H(+) symporter AroP |
| ? | NC_000913 | = 120930 | 97 (1.060) | coding (622/1374 nt) | aroP | aromatic amino acid:H(+) symporter AroP | |||||
| * | ? | NC_000913 | = 2919678 | 106 (1.100) | 3 (0.030) | 3/264 | 7.9 | 3.1% | coding (1069/1341 nt) | gudX | glucarate dehydratase‑related protein |
| ? | NC_000913 | = 2919784 | 84 (0.910) | coding (963/1341 nt) | gudX | glucarate dehydratase‑related protein | |||||
| * | ? | NC_000913 | 535313 = | 73 (0.750) | 3 (0.030) | 3/278 | 8.2 | 3.8% | coding (1398/1782 nt) | gcl | glyoxylate carboligase |
| ? | NC_000913 | 535384 = | 77 (0.800) | coding (1469/1782 nt) | gcl | glyoxylate carboligase | |||||