mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 3,350,618 | 0 | T | C | 40.5% | 16.7 / 47.9 | 42 | noncoding (42/121 nt) | arcZ | small regulatory RNA ArcZ |
| * | NC_000913 | 888,014 | 0 | T | G | 39.5% | 45.6 / 16.9 | 38 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,206,435 | 0 | C | T | 38.9% | 13.3 / 11.0 | 18 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,512 | 0 | C | A | 32.1% | 60.9 / 12.6 | 28 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 30.0% | 70.9 / 13.8 | 40 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 27.1% | 81.8 / 16.2 | 48 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,404,218 | 0 | T | G | 25.6% | 75.3 / 10.9 | 39 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 57.7 / 16.0 | 32 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 266,009 | 0 | A | C | 24.7% | 168.2 / 13.3 | 77 | F27V (TTC→GTC) | ykfB | CP4‑6 prophage; protein YkfB |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.1% | 82.8 / 11.1 | 39 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,207,908 | 1 | . | G | 21.2% | 146.1 / 58.8 | 66 | coding (408/630 nt) | ycfK | e14 prophage; protein StfP |
| 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 | 48 (0.880) | 8 (0.160) | 8/258 | 3.5 | 14.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 48 (0.940) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 11 (0.210) | 7/260 | 3.8 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 14 (0.280) | 5/256 | 4.5 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.080) | 3/202 | 4.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4628780 | NA (NA) | 3 (0.060) | 3/240 | 5.2 | NA | noncoding (37/37 nt) | other | REP354b |
| ? | NC_000913 | = 4633089 | NA (NA) | intergenic (+3/+144) | trpR/yjjX | DNA‑binding transcriptional repressor TrpR/ITPase/XTPase | |||||
| * | ? | NC_000913 | = 502900 | 34 (0.620) | 3 (0.060) | 3/272 | 5.6 | 8.5% | coding (339/1677 nt) | ybaL | putative transporter YbaL |
| ? | NC_000913 | 502904 = | 31 (0.580) | coding (335/1677 nt) | ybaL | putative transporter YbaL | |||||