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 | 3,556,205 | 0 | A | C | 41.4% | 27.6 / 14.9 | 29 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 37.8% | 67.6 / 24.2 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 33.3% | 38.2 / 12.9 | 30 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 650,809 | 0 | T | G | 30.9% | 55.9 / 18.1 | 42 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.4% | 117.5 / 53.9 | 69 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,404,218 | 0 | T | G | 29.3% | 70.5 / 11.6 | 41 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,223,593 | 0 | T | G | 29.1% | 95.1 / 11.4 | 55 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 4,604,344 | 0 | C | T | 28.9% | 134.6 / 34.6 | 76 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,287,719 | 0 | T | A | 27.5% | 97.0 / 21.6 | 51 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 27.0% | 79.9 / 10.1 | 37 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.6% | 75.4 / 11.7 | 43 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.8% | 110.6 / 25.0 | 57 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 501,564 | 0 | A | C | 22.2% | 48.1 / 11.8 | 27 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.9% | 137.2 / 17.0 | 64 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,240,985 | 0 | T | G | 21.4% | 122.9 / 13.3 | 56 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 4,098,155 | 0 | A | C | 20.8% | 155.6 / 10.8 | 72 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.5% | 170.6 / 21.7 | 78 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 2,782,509 | 0 | A | C | 20.0% | 177.4 / 15.4 | 80 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| 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 = | 65 (0.860) | 12 (0.170) | 11/258 | 3.9 | 14.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 84 (1.190) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207790 = | 97 (1.280) | 11 (0.160) | 9/244 | 4.3 | 13.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 56 (0.840) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 89 (1.180) | 8 (0.120) | 8/244 | 4.6 | 10.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 55 (0.820) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 58 (0.770) | 8 (0.110) | 8/258 | 4.8 | 10.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 84 (1.190) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3522817 | 69 (0.910) | 3 (0.040) | 3/270 | 7.1 | 4.2% | intergenic (‑66/‑54) | hofM/mrcA | DNA utilization protein HofM/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| ? | NC_000913 | 3522821 = | 68 (0.920) | intergenic (‑70/‑50) | hofM/mrcA | DNA utilization protein HofM/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA | |||||
| * | ? | NC_000913 | = 1258744 | 77 (1.020) | 3 (0.040) | 3/272 | 7.1 | 3.8% | intergenic (‑231/‑47) | pth/ychH | peptidyl‑tRNA hydrolase/stress‑induced protein |
| ? | NC_000913 | 1258748 = | 75 (1.010) | intergenic (‑235/‑43) | pth/ychH | peptidyl‑tRNA hydrolase/stress‑induced protein | |||||