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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.7% | 47.8 / 30.7 | 48 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 40.0% | 47.1 / 19.9 | 30 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 31.7% | 66.4 / 12.1 | 41 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,512,048 | 0 | A | C | 30.0% | 75.1 / 10.2 | 40 | L123V (TTG→GTG) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| * | NC_000913 | 4,633,383 | 0 | A | G | 29.5% | 81.8 / 46.4 | 61 | G121G (GGT→GGC) | yjjX | ITPase/XTPase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.6% | 48.4 / 10.7 | 28 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,844,219 | 0 | T | G | 27.3% | 123.4 / 13.1 | 55 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 2,406,509 | 0 | G | A | 27.2% | 162.4 / 63.7 | 92 | Q45* (CAA→TAA) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| * | NC_000913 | 372,640 | 0 | T | G | 26.8% | 92.1 / 10.6 | 41 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 26.7% | 135.1 / 17.1 | 60 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.5% | 105.6 / 21.4 | 47 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 103.3 / 12.5 | 44 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,195,080 | 0 | A | G | 24.6% | 122.5 / 40.6 | 69 | intergenic (‑215/+17) | sibD/sibE | small RNA SibD/small RNA SibE |
| * | NC_000913 | 4,568,512 | 0 | C | A | 23.3% | 112.7 / 10.3 | 43 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.9% | 152.6 / 37.5 | 73 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,287,719 | 0 | T | A | 20.4% | 112.3 / 12.3 | 44 | 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 = | 35 (0.560) | 12 (0.210) | 11/258 | 3.1 | 22.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 51 (0.870) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 60 (0.960) | 10 (0.180) | 10/244 | 3.2 | 15.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 55 (1.000) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 34 (0.540) | 10 (0.170) | 9/258 | 3.6 | 19.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 51 (0.870) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3021050 | 54 (0.870) | 3 (0.050) | 3/268 | 6.0 | 5.4% | coding (511/780 nt) | ygfM | putative oxidoreductase |
| ? | NC_000913 | 3021055 = | 53 (0.870) | coding (516/780 nt) | ygfM | putative oxidoreductase | |||||