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 24 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 | 50.0% | 21.2 / 49.2 | 56 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 49.2% | 22.0 / 88.8 | 63 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 83,049 | 0 | C | A | 33.3% | 263.0 / 128.8 | 132 | A161S (GCC→TCC) | leuA | 2‑isopropylmalate synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 75.1 / 27.0 | 39 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.5% | 124.6 / 50.5 | 80 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 650,809 | 0 | T | G | 29.4% | 89.1 / 12.0 | 52 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 786,855 | 0 | A | C | 29.3% | 107.3 / 22.7 | 58 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 445,558 | 0 | A | C | 27.8% | 65.3 / 13.5 | 36 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 501,575 | 0 | A | C | 27.8% | 68.7 / 11.2 | 36 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,001,918 | 0 | A | C | 26.2% | 126.6 / 18.2 | 61 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 25.9% | 120.8 / 23.4 | 58 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 25.8% | 152.3 / 19.5 | 66 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 646,747 | 0 | T | G | 25.5% | 93.7 / 18.8 | 47 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 1,679,688 | 0 | T | G | 25.0% | 150.5 / 21.5 | 73 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| * | NC_000913 | 4,098,155 | 0 | A | C | 24.7% | 151.5 / 15.1 | 73 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 376,401 | 0 | T | G | 23.9% | 198.6 / 20.5 | 92 | L315V (TTG→GTG) | mhpT | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.7% | 282.0 / 14.1 | 132 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 175,694 | 0 | T | G | 23.4% | 135.2 / 15.6 | 64 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 3,274,865 | 0 | T | G | 22.4% | 134.5 / 11.8 | 58 | T15P (ACC→CCC) | garP | galactarate/glucarate/glycerate transporter GarP |
| * | NC_000913 | 4,580,095 | 0 | A | C | 22.2% | 117.4 / 14.7 | 54 | G456G (GGT→GGG) | hsdS | type I restriction enzyme EcoKI specificity protein |
| 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 | 4373295 = | NA (NA) | 19 (0.230) | 13/256 | 3.8 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | = 1396330 | NA (NA) | 6 (0.070) +G |
6/268 | 6.1 | 4.8% | noncoding (287/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428503 | 121 (1.370) | noncoding (292/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 8 (0.090) +T |
6/274 | 6.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 15387 = | NA (NA) | 4 (0.060) | 4/224 | 6.3 | 10.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 16732 = | 33 (0.450) | intergenic (+175/+19) | insL‑1/hokC | IS186/IS421 transposase/protein HokC | |||||
| * | ? | NC_000913 | = 4542690 | 57 (0.640) | 3 (0.040) | 3/258 | 7.4 | 4.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 68 (0.810) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3621328 = | NA (NA) | 3 (0.030) | 3/268 | 7.5 | 100% | coding (2137/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3622058 | 0 (0.000) | coding (2867/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 732449 | 120 (1.340) | 3 (0.030) | 3/268 | 7.5 | 2.5% | coding (2867/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 3621328 = | NA (NA) | coding (2137/4236 nt) | rhsB | rhs element protein RhsB | |||||