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 (highest frequency 20 of 25 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 | 40.0% | 104.0 / 57.6 | 90 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 31.1% | 73.3 / 20.6 | 45 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.6% | 91.5 / 10.3 | 49 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.0% | 132.0 / 19.6 | 70 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.0% | 75.5 / 24.0 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,745,397 | 0 | A | C | 28.6% | 123.5 / 11.5 | 79 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.0% | 87.6 / 12.6 | 50 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.0% | 216.2 / 16.1 | 118 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 888,014 | 0 | T | G | 27.7% | 153.2 / 25.9 | 83 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,401,459 | 0 | T | C | 26.9% | 142.6 / 23.4 | 78 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 3,492,017 | 0 | T | G | 24.8% | 236.1 / 21.3 | 109 | N94T (AAC→ACC) | ppiA | peptidyl‑prolyl cis‑trans isomerase A |
| * | NC_000913 | 501,575 | 0 | A | C | 24.6% | 115.0 / 19.1 | 57 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,429,984 | 0 | T | G | 24.5% | 206.0 / 31.1 | 98 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,747,132 | 0 | G | A | 24.1% | 117.3 / 16.6 | 58 | A17T (GCC→ACC) | lyxK | L‑xylulose kinase |
| * | NC_000913 | 753,125 | 0 | T | A | 22.7% | 186.2 / 17.0 | 75 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 22.3% | 223.5 / 31.5 | 94 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 3,844,219 | 0 | T | G | 22.3% | 239.3 / 18.3 | 103 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.6% | 184.0 / 42.2 | 88 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 21.4% | 161.0 / 13.8 | 56 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 501,564 | 0 | A | C | 21.3% | 129.4 / 23.7 | 61 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 126 (1.080) | 26 (0.250) | 22/246 | 3.0 | 19.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 99 (0.960) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 107 (0.920) | 16 (0.150) | 14/260 | 4.8 | 12.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 121 (1.110) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 119 (1.020) | 6 (0.060) | 5/260 | 7.9 | 4.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 122 (1.120) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1424349 | 112 (0.960) | 4 (0.040) | 4/262 | 8.5 | 3.0% | coding (568/1458 nt) | trkG | Rac prophage; K(+) transporter TrkG |
| ? | NC_000913 | = 1424435 | 152 (1.380) | coding (654/1458 nt) | trkG | Rac prophage; K(+) transporter TrkG | |||||
| * | ? | NC_000913 | 3878636 = | 140 (1.200) | 3 (0.030) | 3/260 | 9.0 | 2.2% | coding (1484/2415 nt) | gyrB | DNA gyrase subunit B |
| ? | NC_000913 | = 3878632 | 133 (1.220) | coding (1488/2415 nt) | gyrB | DNA gyrase subunit B | |||||
| * | ? | NC_000913 | = 1069309 | 89 (0.760) | 3 (0.030) | 3/260 | 9.0 | 3.7% | coding (531/1329 nt) | rutG | pyrimidine:H(+) symporter |
| ? | NC_000913 | = 1069461 | 72 (0.660) | coding (379/1329 nt) | rutG | pyrimidine:H(+) symporter | |||||
| * | ? | NC_000913 | 2481460 = | 135 (1.160) | 3 (0.030) | 3/264 | 9.1 | 2.3% | coding (717/1539 nt) | emrY | tripartite efflux pump membrane subunit EmrY |
| ? | NC_000913 | = 2481456 | 124 (1.120) | coding (721/1539 nt) | emrY | tripartite efflux pump membrane subunit EmrY | |||||
| * | ? | NC_000913 | = 1618107 | 91 (0.780) | 3 (0.030) | 3/266 | 9.1 | 3.2% | coding (1080/1191 nt) | ydeA | L‑arabinose exporter |
| ? | NC_000913 | = 1618188 | 93 (0.830) | coding (1161/1191 nt) | ydeA | L‑arabinose exporter | |||||
| * | ? | NC_000913 | = 153209 | 128 (1.100) | 3 (0.030) | 3/264 | 9.1 | 2.7% | coding (2218/2598 nt) | htrE | putative fimbrial usher protein HtrE |
| ? | NC_000913 | = 153237 | 98 (0.890) | coding (2190/2598 nt) | htrE | putative fimbrial usher protein HtrE | |||||
| * | ? | NC_000913 | = 3889497 | 157 (1.350) | 3 (0.030) | 3/272 | 9.2 | 1.8% | coding (768/1416 nt) | tnaA | tryptophanase |
| ? | NC_000913 | = 3889587 | 174 (1.530) | coding (858/1416 nt) | tnaA | tryptophanase | |||||