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 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,111,747 | 0 | G | T | 44.7% | 51.2 / 32.7 | 38 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 39.2% | 84.3 / 79.6 | 74 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,604,344 | 0 | C | T | 35.1% | 73.8 / 30.9 | 57 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 372,640 | 0 | T | G | 34.0% | 70.1 / 20.3 | 47 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 33.9% | 72.2 / 47.3 | 59 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 29.5% | 66.9 / 13.4 | 44 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.8% | 209.1 / 15.4 | 105 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.6% | 55.8 / 11.1 | 29 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,377,140 | 0 | A | C | 26.4% | 101.5 / 10.3 | 53 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 2,667,126 | 0 | A | C | 25.9% | 110.2 / 15.9 | 58 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 2,140,926 | 0 | A | C | 25.5% | 101.0 / 10.9 | 51 | G229G (GGT→GGG) | asmA | putative assembly protein AsmA |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 121.1 / 18.0 | 52 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 24.6% | 131.1 / 14.3 | 61 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 786,855 | 0 | A | C | 24.5% | 114.4 / 12.0 | 53 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.5% | 125.7 / 18.6 | 51 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 23.4% | 100.2 / 10.3 | 47 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,275,611 | 0 | A | C | 23.3% | 126.2 / 15.0 | 60 | E110D (GAA→GAC) | garD | galactarate dehydratase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.3% | 90.3 / 13.6 | 43 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 22.9% | 97.9 / 19.2 | 48 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 501,564 | 0 | A | C | 22.9% | 67.6 / 14.8 | 35 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| 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 = | 71 (0.770) | 14 (0.160) | 13/258 | 4.3 | 16.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 74 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 62 (0.670) | 11 (0.130) | 11/258 | 4.9 | 14.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 73 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979489 | 96 (1.040) | 18 (0.200) | 7/276 | 6.5 | 15.8% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979486 = | 95 (1.030) | 23 (0.250) | 7/276 | 6.5 | 19.5% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1780251 = | 94 (1.020) | 3 (0.030) | 3/260 | 8.2 | 4.3% | coding (635/765 nt) | ydiQ | putative electron transfer flavoprotein subunit YdiQ |
| ? | NC_000913 | 1846926 = | 45 (0.520) | coding (35/1962 nt) | topB | DNA topoisomerase III | |||||
| * | ? | NC_000913 | = 4439809 | 66 (0.720) | 3 (0.030) | 3/272 | 8.4 | 4.4% | intergenic (+16/+63) | ytfK/ytfL | DUF1107 domain‑containing protein YtfK/putative inner membrane protein |
| ? | NC_000913 | = 4439818 | 64 (0.710) | intergenic (+25/+54) | ytfK/ytfL | DUF1107 domain‑containing protein YtfK/putative inner membrane protein | |||||
| * | ? | NC_000913 | = 2708335 | 117 (1.270) | 3 (0.030) | 3/276 | 8.5 | 2.5% | coding (420/957 nt) | rseB | anti‑sigma factor stabilizing protein RseB |
| ? | NC_000913 | 2708343 = | 114 (1.240) | coding (412/957 nt) | rseB | anti‑sigma factor stabilizing protein RseB | |||||
| * | ? | NC_000913 | = 941425 | 103 (1.120) | 4 (0.040) | 3/276 | 8.5 | 3.7% | coding (467/2445 nt) | dmsA | dimethyl sulfoxide reductase subunit A |
| ? | NC_000913 | 941434 = | 104 (1.130) | coding (476/2445 nt) | dmsA | dimethyl sulfoxide reductase subunit A | |||||