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 (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 | 47.1% | 44.3 / 53.5 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 753,125 | 0 | T | A | 40.5% | 90.1 / 53.3 | 74 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.9% | 137.0 / 40.0 | 65 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 33.3% | 76.4 / 12.2 | 42 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.8% | 110.3 / 23.6 | 61 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.6% | 65.5 / 30.7 | 49 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,114 | 0 | G | T | 32.4% | 154.2 / 23.0 | 72 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 31.5% | 91.8 / 20.2 | 54 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 753,105 | 0 | A | T | 31.2% | 143.6 / 31.5 | 80 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 30.6% | 110.6 / 25.5 | 62 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.3% | 146.8 / 69.5 | 89 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,550,663 | 0 | A | C | 29.3% | 82.9 / 10.1 | 41 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.7% | 237.7 / 11.0 | 114 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 657,676 | 0 | A | C | 25.5% | 115.1 / 10.3 | 51 | V88G (GTG→GGG) | crcB | F(‑) channel |
| * | NC_000913 | 29,496 | 0 | T | A | 25.0% | 79.7 / 12.6 | 36 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.0% | 88.9 / 10.5 | 44 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.7% | 178.2 / 37.5 | 81 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,844,219 | 0 | T | G | 23.2% | 198.9 / 14.7 | 82 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.1% | 147.2 / 14.5 | 52 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,315,936 | 0 | T | A | 22.9% | 139.7 / 12.9 | 61 | K34* (AAA→TAA) | yciG | protein YciG |
| 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 | 59 (0.630) | 17 (0.200) | 16/260 | 3.9 | 21.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 70 (0.800) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207790 = | 122 (1.310) | 16 (0.190) | 15/246 | 3.9 | 16.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 55 (0.670) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 14 (0.160) | 8/262 | 6.3 | 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 | 340035 = | NA (NA) | 8 (0.090) | 5/276 | 8.0 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 2705968 = | 117 (1.260) | 3 (0.030) | 3/272 | 9.1 | 2.7% | coding (1157/1800 nt) | lepA | elongation factor 4 |
| ? | NC_000913 | 2706029 = | 98 (1.080) | coding (1096/1800 nt) | lepA | elongation factor 4 | |||||