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 | 445,558 | 0 | A | C | 40.0% | 64.4 / 27.1 | 50 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,111,747 | 0 | G | T | 37.9% | 102.0 / 44.3 | 58 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 34.1% | 344.7 / 25.3 | 175 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,604,344 | 0 | C | T | 29.8% | 201.6 / 53.2 | 121 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.6% | 187.8 / 25.0 | 85 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 25.7% | 149.9 / 24.9 | 70 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,032,731 | 0 | T | G | 23.1% | 115.2 / 12.5 | 52 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 753,125 | 0 | T | A | 21.2% | 261.5 / 30.3 | 100 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 20.8% | 203.7 / 11.3 | 78 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 20.5% | 169.2 / 25.6 | 73 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,628,625 | 0 | A | C | 20.0% | 218.0 / 10.4 | 80 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| 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 | 129 (1.010) | 15 (0.130) | 15/258 | 4.5 | 10.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 129 (1.080) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2313182 | 149 (1.170) | 5 (0.040) | 5/270 | 7.8 | 3.3% | intergenic (+6/‑306) | micF/rcsD | small regulatory RNA MicF/RcsD phosphotransferase |
| ? | NC_000913 | 2313186 = | 149 (1.190) | intergenic (+10/‑302) | micF/rcsD | small regulatory RNA MicF/RcsD phosphotransferase | |||||
| * | ? | NC_000913 | 4542682 = | 137 (1.070) | 4 (0.030) | 4/258 | 8.1 | 3.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 129 (1.080) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2768338 | 135 (1.060) | 4 (0.030) | 4/270 | 8.3 | 2.9% | coding (629/864 nt) | yfjP | CP4‑57 prophage; putative GTP‑binding protein YfjP |
| ? | NC_000913 | 2768342 = | 135 (1.080) | coding (633/864 nt) | yfjP | CP4‑57 prophage; putative GTP‑binding protein YfjP | |||||
| * | ? | NC_000913 | = 1397622 | 142 (1.110) | 4 (0.030) | 4/266 | 8.3 | 3.0% | coding (258/258 nt) | ynaJ | DUF2534 domain‑containing protein YnaJ |
| ? | NC_000913 | 1397627 = | 126 (1.020) | intergenic (+5/+45) | ynaJ/uspE | DUF2534 domain‑containing protein YnaJ/universal stress protein with a role cellular motility | |||||
| * | ? | NC_000913 | = 633355 | 110 (0.860) | 4 (0.030) | 4/274 | 8.4 | 3.5% | coding (123/1089 nt) | hcxA | hydroxycarboxylate dehydrogenase A |
| ? | NC_000913 | 633359 = | 110 (0.870) | coding (119/1089 nt) | hcxA | hydroxycarboxylate dehydrogenase A | |||||
| * | ? | NC_000913 | 1282904 = | 111 (0.870) | 3 (0.030) | 3/258 | 8.7 | 2.8% | coding (3041/3744 nt) | narG | nitrate reductase A subunit alpha |
| ? | NC_000913 | = 1282898 | 101 (0.850) | coding (3035/3744 nt) | narG | nitrate reductase A subunit alpha | |||||
| * | ? | NC_000913 | = 2628245 | 166 (1.300) | 3 (0.020) | 3/268 | 8.9 | 1.8% | coding (694/2244 nt) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| ? | NC_000913 | 2628250 = | 164 (1.320) | coding (689/2244 nt) | pdeF | cyclic di‑GMP phosphodiesterase PdeF | |||||