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 32 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 | 36.7% | 80.0 / 30.5 | 61 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.3% | 215.4 / 29.5 | 118 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.4% | 142.0 / 27.7 | 74 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,101,507 | 0 | T | G | 32.2% | 161.3 / 17.0 | 88 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 445,558 | 0 | A | C | 32.0% | 76.1 / 31.1 | 50 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,628,625 | 0 | A | C | 31.8% | 110.2 / 29.4 | 63 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.8% | 70.9 / 14.4 | 39 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.3% | 70.9 / 22.1 | 41 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.6% | 173.8 / 52.8 | 91 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,496 | 0 | T | A | 28.4% | 146.0 / 34.7 | 67 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.5% | 85.0 / 10.2 | 40 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,621,118 | 0 | A | C | 26.7% | 97.0 / 12.0 | 45 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| * | NC_000913 | 3,740,909 | 0 | T | G | 25.3% | 193.9 / 26.0 | 91 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 4,580,095 | 0 | A | C | 22.9% | 143.3 / 12.3 | 61 | G456G (GGT→GGG) | hsdS | type I restriction enzyme EcoKI specificity protein |
| * | NC_000913 | 753,125 | 0 | T | A | 22.8% | 151.3 / 12.7 | 57 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 888,014 | 0 | T | G | 22.7% | 148.3 / 10.1 | 66 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,098,155 | 0 | A | C | 22.7% | 257.1 / 21.5 | 110 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.6% | 153.9 / 19.0 | 53 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 372,640 | 0 | T | G | 22.6% | 146.5 / 14.0 | 62 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.2% | 226.3 / 22.7 | 81 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| 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 | 103 (0.950) | 19 (0.190) | 16/258 | 4.3 | 16.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 96 (0.950) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 124 (1.150) | 10 (0.100) | 8/258 | 6.6 | 8.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 96 (0.950) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 22 (0.200) | 8/276 | 7.0 | 13.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2406778 = | 146 (1.350) | intergenic (‑137/‑783) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 3484544 = | 136 (1.260) | 3 (0.030) | 3/256 | 9.1 | 2.3% | coding (55/870 nt) | prkB | putative phosphoribulokinase |
| ? | NC_000913 | = 3484540 | 129 (1.290) | coding (51/870 nt) | prkB | putative phosphoribulokinase | |||||
| * | ? | NC_000913 | = 4137166 | 102 (0.950) | 3 (0.030) | 3/270 | 9.3 | 2.9% | coding (492/618 nt) | yijF | conserved protein YijF |
| ? | NC_000913 | 4137170 = | 101 (0.960) | coding (488/618 nt) | yijF | conserved protein YijF | |||||
| * | ? | NC_000913 | = 3705230 | 147 (1.360) | 3 (0.030) | 3/276 | 9.4 | 2.0% | coding (561/1020 nt) | dppB | dipeptide ABC transporter membrane subunit DppB |
| ? | NC_000913 | 3705235 = | 146 (1.350) | coding (556/1020 nt) | dppB | dipeptide ABC transporter membrane subunit DppB | |||||
| * | ? | NC_000913 | = 118243 | 99 (0.920) | 4 (0.040) | 3/276 | 9.4 | 3.8% | coding (403/894 nt) | nadC | quinolinate phosphoribosyltransferase (decarboxylating) |
| ? | NC_000913 | = 2933842 | 103 (0.950) | intergenic (‑154/‑393) | fucA/fucP | L‑fuculose‑phosphate aldolase/L‑fucose:H(+) symporter | |||||