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 | 45.2% | 45.9 / 46.1 | 62 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 501,575 | 0 | A | C | 40.5% | 45.3 / 17.1 | 37 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 501,564 | 0 | A | C | 36.8% | 47.5 / 22.5 | 38 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.0% | 159.6 / 15.7 | 94 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 32.1% | 37.7 / 15.5 | 28 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,206,435 | 0 | C | T | 31.5% | 80.9 / 28.8 | 54 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.3% | 99.1 / 15.1 | 53 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,444 | 0 | T | A | 28.0% | 98.2 / 13.6 | 50 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,404,215 | 0 | T | G | 26.0% | 136.8 / 30.0 | 73 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.8% | 121.8 / 26.2 | 62 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.5% | 104.8 / 15.8 | 51 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,550,663 | 0 | A | C | 25.4% | 121.9 / 13.4 | 59 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 116.0 / 35.0 | 60 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 650,809 | 0 | T | G | 23.8% | 136.0 / 11.2 | 63 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 23.6% | 164.0 / 12.2 | 72 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 23.2% | 140.5 / 11.8 | 56 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 23.2% | 285.9 / 24.8 | 125 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 1,491,103 | 0 | A | C | 22.2% | 130.5 / 10.3 | 63 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 366,526 | 0 | T | G | 21.4% | 89.7 / 15.5 | 42 | T329P (ACC→CCC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 4,568,512 | 0 | C | A | 20.0% | 187.9 / 18.3 | 65 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| 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 | 1207790 = | 79 (0.950) | 17 (0.230) | 14/246 | 3.2 | 22.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 48 (0.660) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 73 (0.880) | 12 (0.160) | 11/260 | 4.1 | 13.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 82 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 68 (0.820) | 8 (0.100) | 8/260 | 4.9 | 10.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 81 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 74 (0.890) | 23 (0.280) | 7/278 | 5.5 | 23.7% | 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 | = 1979489 | 74 (0.890) | 15 (0.180) | 6/278 | 5.9 | 16.9% | 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 | = 1103283 | 76 (0.920) | 4 (0.050) | 4/272 | 6.7 | 5.1% | intergenic (‑87/‑668) | csgD/csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| ? | NC_000913 | 1103287 = | 74 (0.910) | intergenic (‑91/‑664) | csgD/csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit | |||||
| * | ? | NC_000913 | = 1979489 | 74 (0.890) | 5 (0.060) | 4/278 | 6.8 | 6.3% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 725737 = | 76 (0.920) | 3 (0.040) | 3/260 | 7.1 | 4.0% | coding (1300/2049 nt) | kdpB | K(+) transporting P‑type ATPase subunit KdpB |
| ? | NC_000913 | = 725733 | 73 (0.940) | coding (1304/2049 nt) | kdpB | K(+) transporting P‑type ATPase subunit KdpB | |||||