mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.2% | 61.3 / 49.4 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 39.6% | 129.4 / 23.8 | 91 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,550,663 | 0 | A | C | 34.5% | 85.4 / 28.9 | 58 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 753,125 | 0 | T | A | 31.0% | 100.8 / 28.4 | 58 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.9% | 107.7 / 47.3 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.8% | 94.4 / 19.7 | 52 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 29.8% | 85.8 / 15.8 | 47 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.8% | 77.8 / 14.3 | 47 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 650,809 | 0 | T | G | 29.6% | 101.9 / 14.4 | 54 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 28.3% | 119.3 / 11.7 | 61 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 26.8% | 82.8 / 15.8 | 41 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.3% | 72.7 / 14.4 | 38 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,114 | 0 | G | T | 25.0% | 149.4 / 16.6 | 60 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,568,512 | 0 | C | A | 25.0% | 166.2 / 25.3 | 64 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.2% | 86.6 / 10.6 | 33 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.6% | 147.8 / 15.6 | 55 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 23.5% | 112.7 / 11.0 | 52 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.4% | 156.8 / 16.3 | 77 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 753,105 | 0 | A | T | 22.5% | 171.1 / 14.9 | 71 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 21.8% | 194.5 / 27.7 | 87 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| 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 | 4542682 = | 77 (0.860) | 13 (0.150) | 13/258 | 3.8 | 14.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 77 (0.920) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 95 (1.060) | 13 (0.160) | 12/244 | 3.8 | 15.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 59 (0.740) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 68 (0.760) | 5 (0.060) | 5/258 | 6.3 | 6.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 77 (0.920) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 180634 = | 127 (1.410) | 3 (0.030) | 3/266 | 7.4 | 3.0% | coding (1398/1518 nt) | dgt | dGTP triphosphohydrolase |
| ? | NC_000913 | 180685 = | 72 (0.830) | coding (1449/1518 nt) | dgt | dGTP triphosphohydrolase | |||||
| * | ? | NC_000913 | = 3287914 | 116 (1.300) | 3 (0.030) | 3/274 | 7.5 | 2.5% | coding (489/585 nt) | yraH | putative fimbrial protein YraH |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 3 (0.030) | 3/274 | 7.5 | 2.5% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3287914 | 116 (1.300) | coding (489/585 nt) | yraH | putative fimbrial protein YraH | |||||