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 27 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 | 44.0% | 103.6 / 89.5 | 125 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.8% | 142.7 / 37.5 | 63 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.7% | 259.9 / 22.3 | 143 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 30.8% | 125.2 / 31.7 | 78 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.6% | 131.0 / 26.4 | 73 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.5% | 104.5 / 31.2 | 61 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 501,575 | 0 | A | C | 27.6% | 117.3 / 16.3 | 58 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,667,126 | 0 | A | C | 27.3% | 196.0 / 22.1 | 99 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.1% | 175.6 / 26.8 | 85 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 753,125 | 0 | T | A | 27.0% | 163.6 / 22.4 | 74 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 26.8% | 106.1 / 15.9 | 56 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.6% | 218.3 / 50.6 | 109 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.5% | 222.1 / 27.6 | 102 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,287,719 | 0 | T | A | 26.3% | 240.5 / 51.1 | 114 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 501,564 | 0 | A | C | 25.4% | 125.6 / 17.5 | 59 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 646,747 | 0 | T | G | 25.4% | 150.9 / 24.8 | 71 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.0% | 238.4 / 30.5 | 88 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.7% | 323.4 / 101.4 | 166 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,491,103 | 0 | A | C | 23.8% | 230.7 / 24.8 | 106 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 650,809 | 0 | T | G | 23.2% | 221.1 / 13.2 | 99 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| 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 | = 4542690 | 124 (0.880) | 11 (0.080) | 10/260 | 6.4 | 8.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 134 (1.020) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 128 (0.910) | 10 (0.080) | 9/260 | 6.8 | 7.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 134 (1.020) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 7 (0.050) | 7/278 | 7.8 | 3.4% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 2406701 = | 197 (1.400) | intergenic (‑60/‑860) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 1979399 = | 149 (1.060) | 5 (0.040) | 5/278 | 8.7 | 3.2% | intergenic (‑184/‑354) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 3584195 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 5 (0.040) | 5/278 | 8.7 | 3.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979399 = | 149 (1.060) | intergenic (‑184/‑354) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 1633920 | NA (NA) | 4 (0.030) | 4/272 | 9.1 | 2.8% | coding (299/591 nt) | pinQ | Qin prophage; putative site‑specific recombinase |
| ? | NC_000913 | 1633924 = | 140 (0.990) | coding (303/591 nt) | pinQ | Qin prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 4 (0.030) | 4/276 | 9.2 | 2.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 2406701 = | 197 (1.400) | intergenic (‑60/‑860) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 1219194 = | 225 (1.590) | 4 (0.030) | 3/262 | 9.5 | 2.0% | coding (212/219 nt) | ymgF | inner membrane protein that interacts with cell division proteins |
| ? | NC_000913 | 1219646 = | 175 (1.320) | pseudogene (46/2648 nt) | ycgH | putative transporter component, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 4402297 | 110 (0.780) | 3 (0.020) | 3/270 | 9.7 | 2.3% | coding (260/1260 nt) | hflK | regulator of FtsH protease |
| ? | NC_000913 | 4402575 = | 146 (1.060) | coding (538/1260 nt) | hflK | regulator of FtsH protease | |||||
| * | ? | NC_000913 | = 4359145 | 227 (1.610) | 3 (0.020) | 3/270 | 9.7 | 1.3% | coding (887/1335 nt) | cadB | lysine:cadaverine antiporter |
| ? | NC_000913 | 4359150 = | 224 (1.630) | coding (882/1335 nt) | cadB | lysine:cadaverine antiporter | |||||