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 | 48.1% | 24.5 / 43.0 | 54 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 39.3% | 43.5 / 18.6 | 28 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,550,663 | 0 | A | C | 30.8% | 72.9 / 11.3 | 39 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 2,667,126 | 0 | A | C | 30.6% | 90.0 / 11.7 | 51 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.5% | 186.7 / 12.9 | 96 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 888,014 | 0 | T | G | 30.0% | 95.3 / 14.8 | 50 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.9% | 94.1 / 11.8 | 45 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 26.6% | 139.7 / 23.1 | 64 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.7% | 64.7 / 11.0 | 35 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.4% | 151.7 / 13.3 | 63 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,287,719 | 0 | T | A | 24.6% | 124.2 / 13.3 | 57 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.1% | 156.4 / 13.4 | 65 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 22.6% | 120.3 / 14.9 | 53 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.6% | 187.5 / 12.0 | 74 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 4,296,060 | 0 | C | T | 20.5% | 169.5 / 35.6 | 78 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,261,842 | 0 | T | G | 20.0% | 112.3 / 12.2 | 45 | T12P (ACC→CCC) | prs | ribose‑phosphate diphosphokinase |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 68 (0.910) | 13 (0.200) | 12/246 | 3.6 | 17.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 66 (1.000) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 64 (0.860) | 10 (0.140) | 10/260 | 4.4 | 13.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 73 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3535506 = | 95 (1.280) | 6 (0.090) | 6/258 | 5.8 | 6.8% | coding (363/1353 nt) | envZ | sensory histidine kinase EnvZ |
| ? | NC_000913 | 3535644 = | 77 (1.120) | coding (225/1353 nt) | envZ | sensory histidine kinase EnvZ | |||||
| * | ? | NC_000913 | = 555833 | 68 (0.910) | 4 (0.060) | 4/246 | 6.5 | 5.6% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 74 (1.130) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 4054841 = | 77 (1.040) | 4 (0.060) | 4/258 | 6.7 | 5.5% | coding (438/1410 nt) | glnG | DNA‑binding transcriptional dual regulator NtrC |
| ? | NC_000913 | 4055095 = | 66 (0.960) | coding (184/1410 nt) | glnG | DNA‑binding transcriptional dual regulator NtrC | |||||
| * | ? | NC_000913 | 20447 = | 23 (0.310) | 4 (0.060) | 4/272 | 7.0 | 15.1% | noncoding (117/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 279728 = | NA (NA) | noncoding (203/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 20361 = | NA (NA) | 4 (0.060) | 4/272 | 7.0 | 15.1% | noncoding (203/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 20447 = | 23 (0.310) | noncoding (117/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 2697542 | 80 (1.080) | 3 (0.040) | 3/256 | 7.2 | 3.8% | coding (316/504 nt) | tadA | tRNA adenosine(34) deaminase |
| ? | NC_000913 | = 2697811 | 78 (1.140) | coding (47/504 nt) | tadA | tRNA adenosine(34) deaminase | |||||
| * | ? | NC_000913 | = 2045253 | 67 (0.900) | 11 (0.160) | 3/254 | 7.2 | 15.4% | coding (316/7077 nt) | yeeJ | inverse autotransporter adhesin |
| ? | NC_000913 | = 2045342 | 60 (0.880) | coding (405/7077 nt) | yeeJ | inverse autotransporter adhesin | |||||
| * | ? | NC_000913 | = 1948007 | 96 (1.290) | 3 (0.040) | 3/252 | 7.2 | 3.4% | coding (145/741 nt) | yebC | putative transcriptional regulator YebC |
| ? | NC_000913 | = 1948934 | 82 (1.220) | coding (1589/1773 nt) | aspS | aspartate‑‑tRNA ligase | |||||