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 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,206,435 | 0 | C | T | 39.3% | 52.6 / 44.8 | 56 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 38.0% | 91.5 / 45.2 | 71 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 32.1% | 84.7 / 22.6 | 53 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,512 | 0 | C | A | 31.0% | 134.4 / 27.6 | 58 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.6% | 82.9 / 24.2 | 49 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.4% | 150.4 / 10.4 | 79 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,740,909 | 0 | T | G | 28.4% | 168.7 / 29.8 | 88 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 28.2% | 79.4 / 12.5 | 39 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.6% | 112.2 / 33.6 | 58 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 445,558 | 0 | A | C | 27.3% | 63.0 / 11.6 | 33 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,556,207 | 0 | T | C | 25.4% | 111.1 / 12.8 | 55 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 25.2% | 308.2 / 31.0 | 127 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 29,496 | 0 | T | A | 24.6% | 139.2 / 23.1 | 61 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 23.5% | 95.9 / 11.9 | 34 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.2% | 149.5 / 36.3 | 72 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,098,155 | 0 | A | C | 21.8% | 208.7 / 10.9 | 87 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,101,514 | 0 | G | T | 21.6% | 137.1 / 11.2 | 51 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 650,809 | 0 | T | G | 21.4% | 134.9 / 12.1 | 56 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 21.4% | 171.5 / 16.2 | 70 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 332,991 | 0 | G | T | 21.0% | 219.6 / 26.6 | 81 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| 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 | 375203 = | NA (NA) | 8 (0.100) | 6/216 | 6.3 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4542690 | 97 (0.980) | 8 (0.090) | 7/258 | 6.7 | 7.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 109 (1.180) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 10 (0.120) | 5/226 | 6.9 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 4 (0.050) | 4/216 | 7.2 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 98 (0.990) | 5 (0.050) | 5/258 | 7.6 | 4.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 109 (1.180) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 472551 | 90 (0.910) | 4 (0.040) | 4/274 | 8.4 | 4.3% | intergenic (+134/‑47) | mdlB/glnK | ABC transporter family protein MdlB/nitrogen regulator GlnK |
| ? | NC_000913 | 472556 = | 89 (0.910) | intergenic (+139/‑42) | mdlB/glnK | ABC transporter family protein MdlB/nitrogen regulator GlnK | |||||