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 23 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 | 45.2% | 62.7 / 70.8 | 84 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 38.6% | 74.1 / 34.4 | 57 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.7% | 92.7 / 81.0 | 77 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 36.4% | 62.0 / 23.0 | 33 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 34.0% | 75.9 / 13.4 | 53 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.5% | 59.4 / 15.9 | 40 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,740,909 | 0 | T | G | 32.0% | 75.8 / 14.3 | 50 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 30.8% | 61.7 / 15.6 | 39 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.6% | 56.6 / 19.0 | 36 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,404,218 | 0 | T | G | 30.0% | 86.2 / 14.4 | 50 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.9% | 171.3 / 11.6 | 93 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.0% | 132.6 / 29.1 | 73 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.5% | 101.0 / 11.0 | 51 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 95.1 / 11.2 | 40 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,274,865 | 0 | T | G | 24.6% | 115.0 / 12.5 | 57 | T15P (ACC→CCC) | garP | galactarate/glucarate/glycerate transporter GarP |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.6% | 220.2 / 31.5 | 89 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,577,123 | 0 | A | C | 22.8% | 188.9 / 24.2 | 92 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| * | NC_000913 | 650,809 | 0 | T | G | 22.6% | 122.9 / 15.7 | 63 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 786,855 | 0 | A | C | 21.5% | 142.8 / 13.6 | 65 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 445,558 | 0 | A | C | 20.6% | 66.3 / 11.0 | 34 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 23 (0.360) | 11/216 | 3.4 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 51 (0.620) | 13 (0.170) | 12/258 | 3.9 | 18.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 71 (0.920) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1287084 | 39 (0.470) | 12 (0.170) | 10/236 | 4.0 | 41.9% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 0 (0.000) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 7 (0.120) | 5/190 | 4.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 8 (0.100) | 6/260 | 5.7 | 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 | = 1286906 | 37 (0.450) | 7 (0.100) | 5/236 | 5.8 | 30.7% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 0 (0.000) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4542690 | 49 (0.590) | 5 (0.060) | 5/258 | 6.1 | 7.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 71 (0.920) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.050) | 3/202 | 6.1 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 5 (0.060) +T |
5/274 | 6.4 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 6 (0.070) | 5/274 | 6.4 | 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 | |||||