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 25 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 | 43.0% | 66.1 / 57.1 | 79 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 34.6% | 177.2 / 23.4 | 108 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 650,809 | 0 | T | G | 33.3% | 71.4 / 15.7 | 45 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.6% | 105.2 / 28.2 | 49 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 31.6% | 51.5 / 23.1 | 38 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 31.2% | 87.7 / 23.1 | 48 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.5% | 99.7 / 32.5 | 59 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.5% | 133.1 / 64.4 | 82 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.4% | 100.4 / 22.5 | 56 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.9% | 64.8 / 12.3 | 38 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 28.1% | 109.7 / 22.5 | 57 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 25.4% | 107.8 / 13.2 | 59 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,782,509 | 0 | A | C | 24.5% | 205.1 / 12.7 | 96 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.9% | 181.7 / 27.3 | 67 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 23.7% | 129.5 / 15.0 | 59 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.5% | 148.7 / 15.3 | 68 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,628,625 | 0 | A | C | 23.3% | 91.9 / 12.0 | 44 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,915,866 | 0 | T | G | 23.1% | 115.0 / 10.0 | 52 | Y36S (TAC→TCC) | atpC | ATP synthase F1 complex subunit epsilon |
| * | NC_000913 | 4,032,731 | 0 | T | G | 21.7% | 163.9 / 11.4 | 69 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 4,287,719 | 0 | T | A | 21.4% | 141.5 / 13.2 | 56 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 5 (0.070) | 4/226 | 7.4 | 7.1% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 65 (0.910) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 4542690 | 87 (0.980) | 5 (0.060) | 5/260 | 7.6 | 5.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 89 (1.080) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 12 (0.140) | 5/262 | 7.7 | 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 | 4542682 = | 89 (1.010) | 4 (0.050) | 4/260 | 8.2 | 4.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 90 (1.090) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 235344 | 108 (1.220) | 4 (0.050) | 4/262 | 8.2 | 3.6% | coding (529/723 nt) | yafS | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | = 235428 | 112 (1.350) | coding (613/723 nt) | yafS | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase | |||||
| * | ? | NC_000913 | = 1879834 | 4 (0.050) | 4 (0.050) | 4/272 | 8.4 | 50.0% | coding (115/360 nt) | yeaR | DUF1971 domain‑containing protein YeaR |
| ? | NC_000913 | 2514274 = | NA (NA) | noncoding (2/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 13 (0.150) | 4/278 | 8.5 | 8.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2406778 = | 147 (1.660) | intergenic (‑137/‑783) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 762116 = | 44 (0.500) | 4 (0.050) | 3/250 | 8.6 | 6.7% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinylase |
| ? | NC_000913 | 762340 = | 72 (0.910) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinylase | |||||
| * | ? | NC_000913 | 3406402 = | 80 (0.910) | 3 (0.040) | 3/254 | 8.7 | 3.9% | coding (486/1350 nt) | accC | biotin carboxylase |
| ? | NC_000913 | = 3406398 | 75 (0.930) | coding (482/1350 nt) | accC | biotin carboxylase | |||||
| * | ? | NC_000913 | = 3135413 | 73 (0.830) | 4 (0.050) | 3/260 | 8.8 | 5.1% | coding (959/1500 nt) | pitB | metal phosphate:H(+) symporter PitB |
| ? | NC_000913 | = 3135486 | 80 (0.970) | coding (886/1500 nt) | pitB | metal phosphate:H(+) symporter PitB | |||||