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 23 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 | 40.7% | 60.0 / 38.3 | 60 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.5% | 122.4 / 89.1 | 93 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,101,507 | 0 | T | G | 33.3% | 105.2 / 15.4 | 64 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.2% | 73.8 / 16.3 | 32 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.1% | 124.4 / 30.8 | 74 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,752 | 0 | T | C | 29.5% | 74.0 / 11.1 | 44 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.6% | 156.3 / 26.7 | 63 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 650,809 | 0 | T | G | 27.1% | 136.0 / 20.6 | 70 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.7% | 180.6 / 11.9 | 91 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 372,640 | 0 | T | G | 26.5% | 165.9 / 19.7 | 83 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 29,496 | 0 | T | A | 26.0% | 111.6 / 18.8 | 50 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,906,769 | 0 | A | C | 25.5% | 96.9 / 10.6 | 47 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.5% | 104.2 / 19.6 | 51 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,667,126 | 0 | A | C | 25.4% | 124.8 / 13.2 | 67 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 1,491,098 | 0 | A | C | 25.0% | 126.4 / 12.6 | 68 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.2% | 126.2 / 33.9 | 66 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 23.4% | 134.4 / 19.8 | 64 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,491,103 | 0 | A | C | 21.4% | 138.3 / 14.0 | 70 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 175,694 | 0 | T | G | 21.2% | 135.9 / 11.5 | 66 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 753,125 | 0 | T | A | 21.1% | 136.6 / 10.9 | 52 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| 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 | 50 (0.610) | 16 (0.210) | 15/258 | 3.7 | 21.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 71 (0.930) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 6 (0.110) | 6/190 | 5.1 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 58 (0.710) | 9 (0.120) | 9/258 | 5.3 | 12.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 71 (0.930) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 8 (0.100) | 5/276 | 7.3 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB | |||||
| * | ? | NC_000913 | 1925535 = | 122 (1.490) | 3 (0.040) | 3/264 | 8.2 | 3.0% | coding (96/657 nt) | yobB | putative carbon‑nitrogen hydrolase family protein YobB |
| ? | NC_000913 | 1925908 = | 80 (1.020) | coding (469/657 nt) | yobB | putative carbon‑nitrogen hydrolase family protein YobB | |||||
| * | ? | NC_000913 | = 3658343 | 120 (1.460) | 3 (0.040) | 3/272 | 8.3 | 2.6% | intergenic (‑289/‑23) | arrS/gadE | small regulatory RNA ArrS/DNA‑binding transcriptional activator GadE |
| ? | NC_000913 | 3658586 = | 107 (1.320) | coding (221/528 nt) | gadE | DNA‑binding transcriptional activator GadE | |||||
| * | ? | NC_000913 | 1857953 = | 92 (1.120) | 3 (0.040) | 3/274 | 8.4 | 3.4% | coding (881/1044 nt) | ydjJ | putative zinc‑binding dehydrogenase YdjJ |
| ? | NC_000913 | 4512718 = | 80 (0.980) | coding (692/999 nt) | fecC | ferric citrate ABC transporter membrane subunit FecC | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 4 (0.050) +T |
3/274 | 8.4 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||