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 | 3,931,161 | 0 | C | A | 58.2% | ‑6.3 / 142.8 | 79 | intergenic (‑68/‑155) | ravA/kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| * | NC_000913 | 3,632,338 | 0 | G | A | 44.5% | 90.3 / 215.0 | 164 | H85Y (CAT→TAT) | yhiJ | DUF4049 domain‑containing protein YhiJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 40.5% | 45.2 / 24.7 | 42 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 38.1% | 48.8 / 30.6 | 42 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.4% | 101.0 / 46.4 | 77 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 35.7% | 49.1 / 23.2 | 42 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.3% | 105.6 / 29.5 | 67 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.0% | 165.1 / 14.4 | 90 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,775,467 | 0 | A | C | 26.7% | 74.1 / 10.3 | 45 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.1% | 162.6 / 57.0 | 88 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,628,649 | 0 | A | C | 25.7% | 152.2 / 18.1 | 74 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 650,809 | 0 | T | G | 25.5% | 84.3 / 11.5 | 47 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.4% | 143.1 / 23.0 | 71 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 24.5% | 115.9 / 17.6 | 49 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.3% | 105.1 / 12.7 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.2% | 187.2 / 21.5 | 66 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,401,459 | 0 | T | C | 22.0% | 115.1 / 12.0 | 59 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.1% | 109.5 / 19.3 | 52 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,568,512 | 0 | C | A | 20.3% | 213.2 / 22.1 | 69 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.0% | 130.8 / 10.4 | 60 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| 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 | 61 (0.740) | 16 (0.210) | 13/258 | 4.1 | 17.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 95 (1.230) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 63 (0.760) | 8 (0.100) | 8/258 | 5.7 | 9.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 96 (1.250) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1009157 = | 72 (0.870) | 3 (0.040) | 3/254 | 7.9 | 4.3% | coding (1314/2109 nt) | rlmL | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase |
| ? | NC_000913 | 1009542 = | 67 (0.880) | coding (1699/2109 nt) | rlmL | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase | |||||
| * | ? | NC_000913 | = 4492090 | 113 (1.370) | 3 (0.040) | 3/274 | 8.3 | 2.9% | coding (436/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter |
| ? | NC_000913 | = 4492168 | 91 (1.110) | coding (358/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter | |||||