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 | 3,364,764 | 0 | T | C | 55.2% | 84.6 / 294.2 | 223 | V653A (GTA→GCA) | yhcD | putative fimbrial usher protein YhcD |
| * | NC_000913 | 1,097,392 | 1 | . | G | 50.0% | 4.4 / 10.5 | 8 | intergenic (+563/+173) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 4,296,060 | 0 | C | T | 44.6% | ‑4.1 / 71.0 | 56 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,568,504 | 0 | T | G | 42.9% | 117.4 / 19.6 | 86 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,428,271 | 0 | A | C | 41.9% | 81.8 / 188.9 | 105 | S152S (TCT→TCG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 4,296,042 | 0 | C | T | 41.5% | 23.9 / 56.9 | 53 | intergenic (+248/+394) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 41.0% | 59.1 / 29.3 | 39 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 40.7% | 55.8 / 41.8 | 59 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 650,809 | 0 | T | G | 36.2% | 68.7 / 18.5 | 47 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,427,783 | 0 | A | G | 34.7% | 77.4 / 69.5 | 72 | V315A (GTG→GCG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.3% | 44.9 / 16.4 | 33 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,664,896 | 0 | T | G | 28.9% | 87.1 / 13.1 | 45 | G169G (GGT→GGG) | yfhR | putative peptidase |
| * | NC_000913 | 4,295,929 | 0 | T | C | 28.0% | 37.1 / 13.6 | 25 | intergenic (+135/+507) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 753,125 | 0 | T | A | 27.9% | 86.8 / 14.0 | 43 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 29,496 | 0 | T | A | 26.1% | 105.0 / 17.6 | 47 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.0% | 159.2 / 17.0 | 72 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,926,366 | 0 | A | C | 24.7% | 155.5 / 16.7 | 73 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.1% | 143.7 / 19.8 | 54 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,428,424 | 0 | A | G | 21.7% | 145.4 / 34.6 | 69 | D101D (GAT→GAC) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 3,531,440 | 0 | A | C | 20.7% | 208.8 / 11.4 | 83 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| 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 | = 4542690 | 64 (0.930) | 11 (0.170) | 10/258 | 3.7 | 17.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 47 (0.730) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 63 (0.920) | 10 (0.160) | 10/258 | 3.7 | 15.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 47 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.110) | 4/224 | 5.3 | 7.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 71 (1.280) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 4 (0.070) | 3/226 | 5.8 | 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 | = 3923228 | 77 (1.240) | 14 (0.220) +CACCAGCT |
3/234 | 6.0 | 15.2% | coding (453/624 nt) | rsmG | 16S rRNA m(7)G527 methyltransferase |
| ? | NC_000913 | 3923229 = | 81 (1.180) | coding (452/624 nt) | rsmG | 16S rRNA m(7)G527 methyltransferase | |||||