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 | 4,604,344 | 0 | C | T | 40.7% | 79.2 / 58.3 | 81 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 650,809 | 0 | T | G | 31.0% | 108.3 / 19.1 | 58 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.0% | 197.0 / 15.3 | 100 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 30.8% | 65.4 / 17.5 | 39 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.3% | 110.5 / 26.3 | 58 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.6% | 57.1 / 16.2 | 35 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 501,564 | 0 | A | C | 26.7% | 94.3 / 17.0 | 45 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,240,985 | 0 | T | G | 26.3% | 160.9 / 28.1 | 76 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 25.5% | 114.7 / 13.8 | 51 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.4% | 114.8 / 26.8 | 55 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 25.4% | 129.0 / 10.2 | 59 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 4,429,984 | 0 | T | G | 24.3% | 163.2 / 24.1 | 70 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.2% | 204.1 / 55.1 | 99 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,098,155 | 0 | A | C | 22.0% | 236.7 / 17.8 | 100 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,511,871 | 0 | C | A | 21.6% | 146.6 / 28.1 | 51 | A158A (GCG→GCT) | yhfZ | putative DNA‑binding transcriptional regulator YhfZ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 20.7% | 162.8 / 12.3 | 58 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 34 (0.510) | 12/190 | 3.4 | 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 | 4373295 = | NA (NA) | 22 (0.240) | 15/256 | 3.9 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 375103 = | NA (NA) | 34 (0.350) +T |
14/274 | 4.4 | NA | noncoding (16/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 16 (0.240) | 8/190 | 4.5 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 377353 = | NA (NA) | 19 (0.250) +30 bp |
7/216 | 5.4 | NA | noncoding (18/37 nt) | other | REP32a |
| ? | NC_000913 | 4325850 = | NA (NA) | intergenic (‑109/+549) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 11 (0.150) | 7/216 | 5.4 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 104 (1.070) | 10 (0.110) | 9/258 | 5.5 | 9.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 103 (1.140) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 16 (0.170) | 10/274 | 5.5 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 12 (0.150) | 7/226 | 5.6 | 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 | = 375165 | NA (NA) | 6 (0.090) | 5/192 | 5.7 | NA | noncoding (33/34 nt) | other | REP31e |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||