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 | 372,640 | 0 | T | G | 36.2% | 76.6 / 24.8 | 58 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 34.4% | 126.3 / 45.3 | 90 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.6% | 61.4 / 27.8 | 46 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.4% | 195.9 / 15.0 | 104 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 29,496 | 0 | T | A | 28.3% | 122.9 / 22.6 | 60 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,401,459 | 0 | T | C | 27.9% | 97.9 / 20.2 | 61 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 501,575 | 0 | A | C | 27.0% | 69.0 / 10.5 | 37 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,068,173 | 0 | T | G | 26.1% | 136.5 / 12.6 | 69 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 753,125 | 0 | T | A | 25.9% | 119.9 / 18.1 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 25.5% | 188.9 / 14.9 | 98 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.4% | 124.0 / 24.9 | 63 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.0% | 135.6 / 14.9 | 65 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 888,014 | 0 | T | G | 23.8% | 130.5 / 10.9 | 63 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 650,809 | 0 | T | G | 22.0% | 99.7 / 11.1 | 50 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.0% | 206.7 / 47.4 | 100 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 20.9% | 93.8 / 10.9 | 43 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,114 | 0 | G | T | 20.3% | 164.4 / 12.0 | 59 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 81 (0.970) | 7 (0.090) | 7/260 | 5.8 | 8.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 77 (0.980) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 89 (1.060) | 6 (0.080) | 6/260 | 6.2 | 6.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 78 (1.000) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4492079 | 127 (1.520) | 4 (0.050) | 4/262 | 7.2 | 3.3% | coding (447/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter |
| ? | NC_000913 | = 4492173 | 113 (1.430) | coding (353/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter | |||||
| * | ? | NC_000913 | = 268964 | 103 (1.230) | 3 (0.040) | 3/262 | 7.7 | 2.9% | intergenic (‑4/+325) | ykfA/perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR |
| ? | NC_000913 | = 269030 | 101 (1.280) | intergenic (‑70/+259) | ykfA/perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR | |||||
| * | ? | NC_000913 | 137535 = | 101 (1.210) | 3 (0.040) | 3/262 | 7.7 | 3.2% | coding (453/1551 nt) | cueO | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
| ? | NC_000913 | 137827 = | 88 (1.120) | coding (745/1551 nt) | cueO | cuprous oxidase/multicopper oxidase with role in copper homeostasis | |||||
| * | ? | NC_000913 | = 3619785 | NA (NA) | 3 (0.040) | 3/270 | 7.9 | 100% | coding (594/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3619790 = | 0 (0.000) | coding (599/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 730181 = | 23 (0.270) | 3 (0.040) | 3/270 | 7.9 | 11.8% | coding (599/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | = 3619785 | NA (NA) | coding (594/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 627519 | 69 (0.820) | 3 (0.040) | 3/272 | 7.9 | 4.4% | coding (1450/1611 nt) | entE | 2,3‑dihydroxybenzoate‑AMP ligase |
| ? | NC_000913 | 627525 = | 63 (0.770) | coding (1456/1611 nt) | entE | 2,3‑dihydroxybenzoate‑AMP ligase | |||||
| * | ? | NC_000913 | = 3602247 | 109 (1.300) | 3 (0.040) | 3/276 | 8.0 | 2.8% | coding (501/669 nt) | ftsE | cell division protein FtsE |
| ? | NC_000913 | 3602728 = | 99 (1.190) | coding (20/669 nt) | ftsE | cell division protein FtsE | |||||
| * | ? | NC_000913 | 2326698 = | 73 (0.870) | 3 (0.040) | 3/276 | 8.0 | 4.6% | coding (590/1185 nt) | atoB | acetyl‑CoA acetyltransferase |
| ? | NC_000913 | = 2326895 | 51 (0.610) | coding (787/1185 nt) | atoB | acetyl‑CoA acetyltransferase | |||||