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 | 3,556,207 | 0 | T | C | 36.2% | 60.5 / 20.3 | 47 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 36.1% | 66.1 / 43.6 | 61 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 35.8% | 76.6 / 39.2 | 67 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 32.8% | 90.6 / 26.3 | 61 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.1% | 80.0 / 16.2 | 45 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 30.2% | 97.0 / 27.0 | 53 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,726,177 | 0 | G | T | 27.3% | 49.0 / 13.1 | 22 | noncoding (12/120 nt) | rrfG | 5S ribosomal RNA |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.1% | 94.4 / 18.6 | 48 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 25.8% | 263.2 / 16.5 | 133 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,377,140 | 0 | A | C | 25.3% | 169.5 / 10.7 | 75 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.5% | 98.2 / 23.9 | 49 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.5% | 195.6 / 18.9 | 85 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.9% | 154.4 / 22.0 | 61 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.9% | 96.3 / 12.0 | 35 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,350,853 | 0 | A | C | 22.1% | 170.3 / 15.2 | 68 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| * | NC_000913 | 1,335,691 | 0 | T | G | 21.1% | 173.1 / 14.0 | 77 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 3,274,865 | 0 | T | G | 20.9% | 172.1 / 12.0 | 67 | T15P (ACC→CCC) | garP | galactarate/glucarate/glycerate transporter GarP |
| * | NC_000913 | 4,451,570 | 0 | A | C | 20.7% | 209.8 / 11.1 | 82 | E171D (GAA→GAC) | ytfR | galactofuranose ABC transporter putative ATP binding subunit |
| * | NC_000913 | 3,240,985 | 0 | T | G | 20.0% | 187.3 / 15.4 | 75 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 9 (0.120) | 8/224 | 5.2 | 10.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 74 (0.990) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 15 (0.220) | 6/202 | 5.5 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 64 (0.690) | 9 (0.100) | 8/258 | 5.9 | 11.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 80 (0.930) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 14 (0.170) +GAACGCCTTATCCGGT |
6/244 | 6.4 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 8 (0.090) +T |
7/274 | 6.5 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4542690 | 56 (0.610) | 7 (0.080) | 6/258 | 6.7 | 9.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 80 (0.930) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374965 | NA (NA) | 4 (0.050) | 4/234 | 7.2 | NA | intergenic (+84/‑494) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | = 508781 | NA (NA) | intergenic (+222/+94) | ybaQ/copA | putative DNA‑binding transcriptional regulator YbaQ/Cu(+) exporting P‑type ATPase | |||||
| * | ? | NC_000913 | = 1816202 | NA (NA) | 4 (0.050) | 4/248 | 7.4 | NA | noncoding (17/34 nt) | other | REP129a |
| ? | NC_000913 | = 1816355 | NA (NA) | noncoding (11/30 nt) | other | REPt129c | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 11 (0.150) | 3/216 | 7.4 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 381681 = | NA (NA) | 6 (0.070) | 4/258 | 7.6 | NA | noncoding (422/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381753 = | NA (NA) | noncoding (494/1331 nt) | IS2 | repeat region | |||||