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 | 3,206,435 | 0 | C | T | 40.0% | 33.2 / 30.5 | 40 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 39.3% | 25.8 / 12.1 | 28 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 37.0% | 104.4 / 14.2 | 74 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,444 | 0 | T | A | 35.7% | 55.5 / 22.7 | 42 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.9% | 52.6 / 22.0 | 43 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.8% | 94.2 / 57.5 | 67 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 32.4% | 68.6 / 14.0 | 37 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.4% | 78.3 / 17.5 | 34 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 29.2% | 81.9 / 18.6 | 48 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.8% | 63.0 / 21.0 | 41 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.8% | 113.8 / 13.4 | 42 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,287,719 | 0 | T | A | 20.5% | 80.8 / 11.0 | 39 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 20.0% | 168.0 / 10.3 | 80 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| 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 | 29 (0.510) | 10 (0.190) | 10/260 | 3.5 | 21.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 44 (0.830) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4214391 = | 54 (0.960) | 3 (0.060) | 3/256 | 6.1 | 5.3% | coding (112/930 nt) | metA | homoserine O‑succinyltransferase |
| ? | NC_000913 | 4214577 = | 58 (1.120) | coding (298/930 nt) | metA | homoserine O‑succinyltransferase | |||||
| * | ? | NC_000913 | = 4211996 | NA (NA) | 5 (0.090) +CTTACTGCT |
3/260 | 6.2 | 9.7% | noncoding (1954/2904 nt) | rrlE | 23S ribosomal RNA |
| ? | NC_000913 | = 4213166 | 50 (0.890) | intergenic (+7/‑68) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||
| * | ? | NC_000913 | = 4039473 | 31 (0.550) | 5 (0.090) +CTTACTGCT |
3/260 | 6.2 | 11.7% | noncoding (1955/2905 nt) | rrlA | 23S ribosomal RNA |
| ? | NC_000913 | = 4213166 | 50 (0.890) | intergenic (+7/‑68) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||
| * | ? | NC_000913 | = 3945657 | 26 (0.460) | 5 (0.090) +CTTACTGCT |
3/260 | 6.2 | 12.3% | noncoding (1954/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | = 4213166 | 50 (0.890) | intergenic (+7/‑68) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||
| * | ? | NC_000913 | = 4121631 | 67 (1.190) | 3 (0.050) | 3/274 | 6.4 | 4.3% | coding (117/1332 nt) | hslU | ATPase component of the HslVU protease |
| ? | NC_000913 | 4121635 = | 66 (1.190) | coding (113/1332 nt) | hslU | ATPase component of the HslVU protease | |||||
| * | ? | NC_000913 | = 3603196 | 54 (0.960) | 3 (0.050) | 3/274 | 6.4 | 5.0% | coding (1048/1494 nt) | ftsY | signal recognition particle receptor |
| ? | NC_000913 | = 3603282 | 60 (1.080) | coding (962/1494 nt) | ftsY | signal recognition particle receptor | |||||
| * | ? | NC_000913 | = 3664675 | 66 (1.170) | 3 (0.050) | 3/276 | 6.5 | 4.7% | intergenic (‑57/‑189) | gadW/gadY | DNA‑binding transcriptional dual regulator GadW/small regulatory RNA GadY |
| ? | NC_000913 | = 3664781 | 56 (1.000) | intergenic (‑163/‑83) | gadW/gadY | DNA‑binding transcriptional dual regulator GadW/small regulatory RNA GadY | |||||