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 | 1,775,467 | 0 | A | C | 35.5% | 33.0 / 10.8 | 31 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.7% | 79.1 / 24.7 | 49 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,604,344 | 0 | C | T | 34.7% | 113.6 / 40.6 | 75 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.3% | 38.7 / 13.3 | 33 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,101,507 | 0 | T | G | 32.3% | 92.6 / 14.4 | 62 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.1% | 36.2 / 14.3 | 28 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.6% | 111.8 / 10.4 | 72 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 28.6% | 90.0 / 17.2 | 42 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.8% | 100.4 / 14.8 | 36 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,404,218 | 0 | T | G | 26.8% | 96.7 / 16.5 | 56 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 26.7% | 159.5 / 19.7 | 60 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 753,105 | 0 | A | T | 25.6% | 100.9 / 10.7 | 43 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,679,688 | 0 | T | G | 24.1% | 104.9 / 12.8 | 58 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 24.1% | 102.1 / 19.2 | 58 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 646,747 | 0 | T | G | 22.7% | 73.7 / 18.1 | 44 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 22.0% | 97.2 / 11.3 | 50 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.0% | 112.6 / 23.7 | 50 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 20.0% | 88.2 / 11.9 | 45 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| 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 | = 4542690 | 45 (0.640) | 9 (0.140) | 9/258 | 4.1 | 13.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 71 (1.070) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 51 (0.720) | 9 (0.140) | 9/258 | 4.1 | 13.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 72 (1.090) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207790 = | 75 (1.060) | 8 (0.130) | 8/244 | 4.2 | 11.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 62 (0.990) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 15 (0.230) | 8/260 | 4.4 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 4 (0.070) | 3/224 | 5.9 | 5.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 65 (1.130) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 1827135 = | 44 (0.620) | 4 (0.060) | 4/262 | 6.0 | 9.0% | coding (1125/1344 nt) | astB | N‑succinylarginine dihydrolase |
| ? | NC_000913 | = 1827131 | 39 (0.580) | coding (1129/1344 nt) | astB | N‑succinylarginine dihydrolase | |||||