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 | 4,101,507 | 0 | T | G | 41.3% | 57.2 / 16.6 | 46 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.9% | 85.1 / 33.2 | 63 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,628,625 | 0 | A | C | 29.4% | 61.1 / 10.8 | 34 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.0% | 172.4 / 12.7 | 93 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,401,459 | 0 | T | C | 27.8% | 126.3 / 22.1 | 72 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,101,514 | 0 | G | T | 27.3% | 91.7 / 20.9 | 44 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,745,397 | 0 | A | C | 26.7% | 111.4 / 10.4 | 61 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,240,985 | 0 | T | G | 26.5% | 96.3 / 14.4 | 49 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 25.9% | 56.3 / 10.4 | 27 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.0% | 82.5 / 10.4 | 40 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.4% | 123.8 / 19.4 | 45 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.3% | 169.6 / 10.1 | 73 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 1,377,140 | 0 | A | C | 21.4% | 126.8 / 10.4 | 56 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.2% | 143.4 / 31.7 | 66 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.2% | 188.4 / 42.3 | 85 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 20.0% | 107.5 / 12.5 | 45 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| 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 | 55 (0.760) | 6 (0.090) | 6/258 | 5.8 | 11.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 44 (0.650) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 51 (0.700) | 6 (0.090) | 6/258 | 5.8 | 11.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 44 (0.650) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1978494 | 0 (0.000) | 9 (0.120) | 6/276 | 6.2 | 100% | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 187918 = | 54 (0.740) | 4 (0.060) | 4/252 | 6.7 | 7.7% | coding (733/2673 nt) | glnD | PII uridylyltransferase/uridylyl removing enzyme |
| ? | NC_000913 | 188143 = | 47 (0.710) | coding (508/2673 nt) | glnD | PII uridylyltransferase/uridylyl removing enzyme | |||||
| * | ? | NC_000913 | = 4492079 | 120 (1.650) | 4 (0.060) | 3/260 | 7.4 | 3.9% | coding (447/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter |
| ? | NC_000913 | = 4492173 | 82 (1.200) | coding (353/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter | |||||
| * | ? | NC_000913 | 2312061 = | 58 (0.800) | 3 (0.040) | 3/266 | 7.5 | 4.4% | coding (689/1104 nt) | ompC | outer membrane porin C |
| ? | NC_000913 | 2312146 = | 75 (1.070) | coding (604/1104 nt) | ompC | outer membrane porin C | |||||
| * | ? | NC_000913 | 1538789 = | 57 (0.780) | 3 (0.040) | 3/264 | 7.5 | 4.8% | coding (65/1545 nt) | narY | nitrate reductase Z subunit beta |
| ? | NC_000913 | 1538874 = | 65 (0.930) | coding (3717/3741 nt) | narZ | nitrate reductase Z subunit alpha | |||||
| * | ? | NC_000913 | = 3619776 | NA (NA) | 3 (0.040) | 3/274 | 7.6 | 100% | coding (585/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620830 = | 0 (0.000) | coding (1639/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 2273903 | 56 (0.770) | 3 (0.040) | 3/276 | 7.7 | 5.1% | coding (1540/1815 nt) | yejA | putative oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 2273949 | 56 (0.770) | coding (1586/1815 nt) | yejA | putative oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 3 (0.040) | 3/276 | 7.7 | 100% | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101745 = | NA (NA) | intergenic (‑1/+150) | wbbL/insH‑7 | interrupted rhamnosyltransferase WbbL/IS5 transposase and trans‑activator | |||||