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% | 66.9 / 40.5 | 58 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 37.0% | 30.0 / 14.0 | 27 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.0% | 150.2 / 15.4 | 90 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 30.2% | 106.5 / 23.4 | 53 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.2% | 62.9 / 19.0 | 39 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.2% | 99.9 / 15.3 | 39 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.0% | 129.5 / 26.8 | 50 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 27.9% | 109.9 / 15.4 | 61 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 445,558 | 0 | A | C | 27.5% | 70.0 / 15.7 | 40 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.1% | 127.3 / 36.7 | 70 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.7% | 149.4 / 49.7 | 75 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,350,853 | 0 | A | C | 26.5% | 63.5 / 10.1 | 34 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| * | NC_000913 | 2,483,268 | 0 | T | A | 25.9% | 118.4 / 19.8 | 54 | L24F (TTA→TTT) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| * | NC_000913 | 650,809 | 0 | T | G | 25.0% | 123.1 / 13.7 | 60 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 23.9% | 92.1 / 12.9 | 46 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,032,731 | 0 | T | G | 23.1% | 105.9 / 10.7 | 52 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 332,991 | 0 | G | T | 20.4% | 153.6 / 10.4 | 54 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 646,747 | 0 | T | G | 20.0% | 155.9 / 28.2 | 70 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | 62 (0.680) | 12 (0.140) | 10/256 | 5.1 | 15.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 77 (0.900) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 69 (0.760) | 10 (0.120) | 9/256 | 5.4 | 12.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 79 (0.930) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 792418 = | 105 (1.150) | 4 (0.050) | 4/262 | 7.6 | 3.8% | coding (1371/1473 nt) | modF | ABC family protein ModF |
| ? | NC_000913 | = 792413 | 102 (1.170) | coding (1376/1473 nt) | modF | ABC family protein ModF | |||||
| * | ? | NC_000913 | 723100 = | 93 (1.020) | 3 (0.040) | 3/254 | 8.0 | 3.3% | coding (1315/2685 nt) | kdpD | sensory histidine kinase KdpD |
| ? | NC_000913 | = 723096 | 90 (1.060) | coding (1319/2685 nt) | kdpD | sensory histidine kinase KdpD | |||||
| * | ? | NC_000913 | 3540546 = | 99 (1.080) | 3 (0.030) | 3/264 | 8.2 | 3.2% | coding (140/2322 nt) | feoB | Fe(2(+)) transporter FeoB |
| ? | NC_000913 | = 3540542 | 84 (0.960) | coding (136/2322 nt) | feoB | Fe(2(+)) transporter FeoB | |||||
| * | ? | NC_000913 | = 2081271 | 72 (0.790) | 3 (0.030) | 3/266 | 8.2 | 3.8% | intergenic (‑9/+110) | sbmC/dacD | DNA gyrase inhibitor/D‑alanyl‑D‑alanine carboxypeptidase DacD |
| ? | NC_000913 | 2845402 = | 81 (0.910) | coding (1070/1710 nt) | hycE | formate hydrogenlyase subunit HycE | |||||
| * | ? | NC_000913 | = 916723 | 95 (1.040) | 3 (0.030) | 3/270 | 8.3 | 3.3% | coding (251/1659 nt) | ybjD | DUF2813 domain‑containing protein YbjD |
| ? | NC_000913 | 2483350 = | 81 (0.900) | intergenic (‑11/‑405) | emrK/evgA | tripartite efflux pump membrane fusion protein EmrK/DNA‑binding transcriptional activator EvgA | |||||
| * | ? | NC_000913 | = 3027242 | 101 (1.110) | 3 (0.030) | 3/274 | 8.4 | 3.0% | coding (122/1368 nt) | ghxQ | guanine/hypoxanthine transporter GhxQ |
| ? | NC_000913 | 3027249 = | 96 (1.050) | coding (129/1368 nt) | ghxQ | guanine/hypoxanthine transporter GhxQ | |||||