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 21 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 | 51.1% | 33.8 / 124.3 | 90 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 36.4% | 94.1 / 44.0 | 77 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.5% | 160.2 / 21.9 | 107 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.6% | 57.8 / 10.5 | 38 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 30.0% | 49.2 / 12.4 | 40 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.0% | 164.4 / 32.2 | 62 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.7% | 234.3 / 95.6 | 129 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,512,048 | 0 | A | C | 26.5% | 126.4 / 19.6 | 68 | L123V (TTG→GTG) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| * | NC_000913 | 888,014 | 0 | T | G | 26.3% | 138.7 / 16.0 | 76 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,740,909 | 0 | T | G | 25.3% | 156.7 / 23.4 | 84 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.6% | 135.1 / 29.1 | 65 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 24.2% | 164.1 / 23.8 | 66 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.3% | 208.2 / 27.1 | 103 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 753,125 | 0 | T | A | 22.9% | 204.7 / 24.1 | 83 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.4% | 123.2 / 32.9 | 67 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,114 | 0 | G | T | 21.9% | 230.0 / 18.1 | 82 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 21.8% | 259.8 / 20.3 | 124 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 650,809 | 0 | T | G | 21.7% | 119.4 / 15.5 | 60 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 21.5% | 132.0 / 15.6 | 65 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 646,747 | 0 | T | G | 21.0% | 162.0 / 32.2 | 81 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1979646 | 101 (0.880) | 18 (0.160) | 10/276 | 6.2 | 15.1% | intergenic (‑431/‑107) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 128 (1.120) | 9 (0.080) | 8/258 | 6.5 | 7.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 113 (1.060) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 134 (1.170) | 5 (0.050) | 5/258 | 7.8 | 4.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 113 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979646 | 101 (0.880) | 5 (0.040) | 5/276 | 8.1 | 4.7% | intergenic (‑431/‑107) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2030707 = | 108 (0.940) | 4 (0.040) | 4/260 | 8.3 | 3.8% | coding (212/471 nt) | vsr | DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway |
| ? | NC_000913 | = 2030703 | 100 (0.930) | coding (216/471 nt) | vsr | DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway | |||||
| * | ? | NC_000913 | = 2191800 | 149 (1.300) | 4 (0.040) | 4/264 | 8.4 | 2.2% | coding (423/543 nt) | yehD | putative fimbrial protein YehD |
| ? | NC_000913 | 2191946 = | 213 (1.940) | coding (277/543 nt) | yehD | putative fimbrial protein YehD | |||||
| * | ? | NC_000913 | 967030 = | 183 (1.600) | 3 (0.030) | 3/256 | 8.9 | 1.8% | coding (410/1749 nt) | msbA | ATP‑binding lipopolysaccharide transport protein |
| ? | NC_000913 | = 967026 | 164 (1.540) | coding (406/1749 nt) | msbA | ATP‑binding lipopolysaccharide transport protein | |||||
| * | ? | NC_000913 | = 3232447 | 99 (0.860) | 5 (0.040) | 3/270 | 9.1 | 4.9% | coding (783/2019 nt) | fadH | 2,4‑dienoyl‑CoA reductase |
| ? | NC_000913 | 3232453 = | 98 (0.870) | coding (789/2019 nt) | fadH | 2,4‑dienoyl‑CoA reductase | |||||
| * | ? | NC_000913 | = 1327086 | 97 (0.850) | 3 (0.030) | 3/272 | 9.1 | 3.1% | coding (235/876 nt) | rluB | 23S rRNA pseudouridine(2605) synthase |
| ? | NC_000913 | 1327090 = | 90 (0.800) | coding (239/876 nt) | rluB | 23S rRNA pseudouridine(2605) synthase | |||||
| * | ? | NC_000913 | = 686486 | 122 (1.060) | 6 (0.050) | 3/270 | 9.1 | 4.7% | coding (184/741 nt) | gltJ | glutamate/aspartate ABC transporter membrane subunit GltJ |
| ? | NC_000913 | 686491 = | 122 (1.090) | coding (179/741 nt) | gltJ | glutamate/aspartate ABC transporter membrane subunit GltJ | |||||