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 21 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 | 46.7% | 45.0 / 64.0 | 75 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,209,827 | 0 | T | G | 37.9% | 24.7 / 14.5 | 29 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 4,111,747 | 0 | G | T | 34.2% | 88.6 / 29.8 | 41 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.5% | 60.6 / 16.8 | 40 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 445,558 | 0 | A | C | 32.5% | 104.5 / 53.2 | 77 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 29,496 | 0 | T | A | 32.4% | 200.8 / 71.5 | 108 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.8% | 67.3 / 11.0 | 39 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.2% | 91.3 / 16.2 | 53 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.2% | 191.1 / 16.4 | 106 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 501,575 | 0 | A | C | 26.0% | 157.6 / 20.9 | 77 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.5% | 95.6 / 11.1 | 47 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 104.9 / 15.1 | 44 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,740,909 | 0 | T | G | 25.0% | 135.0 / 15.1 | 68 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 24.2% | 192.6 / 22.0 | 100 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.4% | 121.8 / 31.3 | 64 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 650,809 | 0 | T | G | 22.7% | 132.8 / 15.0 | 66 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,335,691 | 0 | T | G | 22.1% | 179.9 / 12.9 | 86 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 372,640 | 0 | T | G | 21.9% | 207.1 / 22.2 | 96 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.8% | 199.6 / 44.2 | 87 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,350,853 | 0 | A | C | 21.0% | 140.9 / 13.9 | 62 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| 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 | 4542682 = | 82 (0.880) | 7 (0.080) | 7/258 | 5.8 | 7.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 99 (1.140) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 341066 = | 161 (1.730) | 3 (0.030) | 3/262 | 7.7 | 1.9% | coding (902/951 nt) | yahI | carbamate kinase‑like protein YahI |
| ? | NC_000913 | = 341061 | 156 (1.770) | coding (897/951 nt) | yahI | carbamate kinase‑like protein YahI | |||||
| * | ? | NC_000913 | = 2730204 | NA (NA) | 3 (0.030) | 3/272 | 7.9 | NA | noncoding (954/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2730208 = | NA (NA) | noncoding (950/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 1428196 | 39 (0.420) | 3 (0.030) | 3/274 | 7.9 | 7.4% | noncoding (599/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | 1428201 = | 36 (0.390) | noncoding (594/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1396643 = | NA (NA) | 3 (0.030) | 3/274 | 7.9 | 7.7% | noncoding (600/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1428200 = | 36 (0.390) | noncoding (595/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1396637 | NA (NA) | 3 (0.030) +G |
3/270 | 7.9 | NA | noncoding (594/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428195 | NA (NA) | noncoding (600/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 274551 | NA (NA) | 3 (0.030) | 3/274 | 7.9 | NA | noncoding (599/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274556 = | NA (NA) | noncoding (594/1195 nt) | IS5 | repeat region | |||||