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 | 4,604,344 | 0 | C | T | 39.7% | 65.2 / 41.3 | 63 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.5% | 54.8 / 22.6 | 40 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 30.0% | 107.5 / 32.2 | 60 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,740,909 | 0 | T | G | 29.3% | 114.6 / 16.3 | 58 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 28.3% | 84.0 / 10.2 | 46 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,068,173 | 0 | T | G | 27.9% | 179.9 / 18.1 | 79 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.9% | 144.9 / 53.9 | 79 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.8% | 111.8 / 16.9 | 41 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 25.4% | 120.0 / 16.0 | 55 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.4% | 138.4 / 11.1 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 646,747 | 0 | T | G | 24.0% | 117.1 / 18.2 | 50 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,003,480 | 0 | A | G | 23.5% | 152.3 / 25.5 | 81 | G289G (GGA→GGG) | xdhB | putative xanthine dehydrogenase FAD‑binding subunit XdhB |
| * | NC_000913 | 332,991 | 0 | G | T | 22.0% | 172.5 / 17.7 | 59 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 366,526 | 0 | T | G | 21.6% | 128.3 / 13.2 | 51 | T329P (ACC→CCC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 4,429,984 | 0 | T | G | 20.8% | 190.4 / 15.3 | 72 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,844,219 | 0 | T | G | 20.0% | 250.3 / 11.8 | 90 | F86V (TTT→GTT) | adeD | adenine deaminase |
| 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 | 70 (0.780) | 16 (0.190) | 13/258 | 4.5 | 15.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 106 (1.260) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 17 (0.260) | 9/202 | 4.5 | 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) | 9 (0.100) +T |
9/274 | 6.0 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 4542682 = | 83 (0.920) | 6 (0.070) | 6/258 | 6.9 | 6.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 107 (1.270) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 4 (0.040) +T |
4/274 | 8.2 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 1653702 = | 101 (1.120) | 3 (0.040) | 3/258 | 8.5 | 3.1% | coding (214/1020 nt) | rspB | putative zinc‑binding dehydrogenase RspB |
| ? | NC_000913 | = 3252190 | NA (NA) | intergenic (+180/‑114) | yqjG/yhaH | glutathionyl‑hydroquinone reductase YqjG/putative inner membrane protein | |||||
| * | ? | NC_000913 | 3371571 = | 100 (1.110) | 3 (0.030) | 3/270 | 8.7 | 2.9% | coding (1004/1491 nt) | nanT | N‑acetylneuraminate:H(+) symporter |
| ? | NC_000913 | = 3534786 | 101 (1.140) | coding (1083/1353 nt) | envZ | sensory histidine kinase EnvZ | |||||
| * | ? | NC_000913 | = 2980541 | 129 (1.430) | 3 (0.030) | 3/272 | 8.7 | 2.3% | coding (95/693 nt) | ygeA | amino acid racemase |
| ? | NC_000913 | 2980546 = | 128 (1.440) | coding (90/693 nt) | ygeA | amino acid racemase | |||||