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 31 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 | 46.5% | 68.1 / 89.3 | 101 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 445,558 | 0 | A | C | 41.3% | 49.6 / 51.2 | 63 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,556,205 | 0 | A | C | 39.0% | 51.1 / 15.3 | 41 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 36.0% | 101.4 / 36.1 | 75 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 34.2% | 87.2 / 24.6 | 41 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.3% | 112.7 / 47.4 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.4% | 191.6 / 22.5 | 119 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 30.4% | 139.4 / 29.9 | 69 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 30.1% | 192.8 / 47.6 | 123 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 29.5% | 100.3 / 16.4 | 61 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 29,496 | 0 | T | A | 27.9% | 133.5 / 28.1 | 61 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,926,366 | 0 | A | C | 27.6% | 157.0 / 25.1 | 87 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.5% | 76.4 / 12.8 | 40 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,101,507 | 0 | T | G | 26.7% | 175.1 / 10.3 | 90 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.4% | 205.4 / 69.6 | 106 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.2% | 101.2 / 33.8 | 61 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 26.1% | 126.9 / 27.7 | 69 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.8% | 123.2 / 26.6 | 62 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,335,691 | 0 | T | G | 25.7% | 131.8 / 14.0 | 74 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.5% | 194.7 / 30.4 | 106 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| 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 | 84 (0.880) | 16 (0.180) | 16/258 | 3.7 | 14.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 115 (1.280) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 100 (1.040) | 9 (0.100) | 8/258 | 6.0 | 7.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 117 (1.300) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 118 (1.230) | 31 (0.320) | 5/276 | 7.6 | 20.8% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 555833 | 107 (1.120) | 3 (0.040) | 3/244 | 8.1 | 3.3% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 82 (0.970) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | = 893089 | 68 (0.710) | 3 (0.030) | 3/272 | 8.6 | 4.2% | coding (133/477 nt) | ybjN | protein YbjN |
| ? | NC_000913 | 893093 = | 71 (0.750) | coding (137/477 nt) | ybjN | protein YbjN | |||||
| * | ? | NC_000913 | = 610860 | 246 (2.560) | 3 (0.030) | 3/272 | 8.6 | 1.2% | coding (1635/2241 nt) | fepA | ferric enterobactin outer membrane transporter |
| ? | NC_000913 | 610864 = | 246 (2.600) | coding (1631/2241 nt) | fepA | ferric enterobactin outer membrane transporter | |||||
| * | ? | NC_000913 | = 1979489 | 116 (1.210) | 14 (0.150) | 3/276 | 8.7 | 10.8% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 5 (0.050) | 3/276 | 8.7 | 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 | = 375160 | NA (NA) | 3 (0.030) +T |
3/274 | 8.7 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||