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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,709,602 | 0 | G | T | 53.1% | 23.8 / 257.0 | 128 | G154V (GGT→GTT) | rsxD | SoxR [2Fe‑2S] reducing system protein RsxD |
| * | NC_000913 | 4,111,747 | 0 | G | T | 39.1% | 76.6 / 36.7 | 46 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.3% | 127.7 / 40.8 | 81 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 501,575 | 0 | A | C | 32.4% | 64.3 / 13.7 | 37 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.2% | 171.2 / 20.1 | 90 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 31.4% | 116.2 / 45.9 | 71 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 30.4% | 70.4 / 12.4 | 46 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.7% | 121.3 / 26.2 | 64 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 501,564 | 0 | A | C | 28.9% | 62.8 / 21.8 | 38 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.9% | 106.1 / 23.3 | 54 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.9% | 210.8 / 71.2 | 108 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,287,719 | 0 | T | A | 25.9% | 180.6 / 39.0 | 85 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 29,496 | 0 | T | A | 25.4% | 116.6 / 22.0 | 55 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.3% | 201.1 / 25.1 | 92 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 646,747 | 0 | T | G | 25.0% | 123.2 / 29.3 | 60 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 753,125 | 0 | T | A | 24.6% | 146.3 / 19.6 | 65 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 24.1% | 125.7 / 10.6 | 58 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 650,809 | 0 | T | G | 24.1% | 188.2 / 21.8 | 83 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,168,966 | 0 | A | C | 22.3% | 215.8 / 22.0 | 95 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.9% | 231.0 / 18.8 | 96 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 13 (0.180) | 11/190 | 3.9 | 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 | 4542682 = | 76 (0.730) | 8 (0.080) | 8/258 | 6.2 | 8.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 100 (1.030) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 75 (0.720) | 7 (0.070) | 7/258 | 6.6 | 7.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 100 (1.030) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 11 (0.110) | 7/260 | 6.6 | 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 | 340035 = | NA (NA) | 8 (0.080) | 7/274 | 6.9 | 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 | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 8 (0.080) | 6/268 | 7.2 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3787895 = | 86 (0.830) | 4 (0.040) | 4/256 | 7.9 | 4.8% | coding (1058/1260 nt) | envC | murein hydrolase activator EnvC |
| ? | NC_000913 | = 3787891 | 80 (0.830) | coding (1054/1260 nt) | envC | murein hydrolase activator EnvC | |||||
| * | ? | NC_000913 | = 4568343 | 129 (1.240) | 3 (0.030) | 3/264 | 8.6 | 2.7% | coding (177/1233 nt) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| ? | NC_000913 | = 4568488 | 97 (0.970) | coding (32/1233 nt) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter | |||||
| * | ? | NC_000913 | 331873 = | 144 (1.380) | 3 (0.030) | 3/264 | 8.6 | 2.1% | coding (72/75 nt) | yahV | protein YahV |
| ? | NC_000913 | 331887 = | 141 (1.420) | intergenic (+11/‑484) | yahV/pdeL | protein YahV/DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL | |||||
| * | ? | NC_000913 | = 4096305 | 131 (1.260) | 3 (0.030) | 3/274 | 8.8 | 2.2% | coding (1144/1470 nt) | rhaB | rhamnulokinase |
| ? | NC_000913 | 4096309 = | 131 (1.270) | coding (1140/1470 nt) | rhaB | rhamnulokinase | |||||