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 | 38.8% | 93.9 / 52.0 | 81 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.7% | 72.8 / 12.0 | 41 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.5% | 240.2 / 20.4 | 131 | 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 | 31.2% | 50.9 / 11.9 | 32 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.2% | 97.5 / 21.6 | 53 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.0% | 86.8 / 24.4 | 40 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 29.4% | 119.2 / 40.7 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 28.6% | 130.1 / 13.1 | 63 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.6% | 71.7 / 12.6 | 42 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 28.6% | 112.4 / 10.5 | 56 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 26.1% | 93.7 / 18.0 | 46 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.8% | 224.6 / 76.9 | 120 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 25.0% | 71.1 / 13.9 | 36 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 650,809 | 0 | T | G | 24.0% | 163.0 / 14.8 | 75 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 23.8% | 153.8 / 17.2 | 64 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.5% | 107.1 / 15.1 | 51 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.2% | 222.0 / 18.3 | 99 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,101,514 | 0 | G | T | 23.2% | 152.6 / 18.3 | 56 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,491,103 | 0 | A | C | 23.0% | 163.2 / 10.5 | 74 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 81 (0.840) | 18 (0.200) | 17/260 | 3.2 | 18.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 86 (0.950) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 77 (0.790) | 16 (0.190) | 14/246 | 3.6 | 18.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 75 (0.880) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 85 (0.880) | 9 (0.100) | 8/260 | 5.4 | 9.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 88 (0.970) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979337 = | 47 (0.490) | 17 (0.180) | 6/278 | 6.4 | 26.6% | intergenic (‑122/‑416) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 535294 = | 141 (1.460) | 6 (0.060) | 5/266 | 6.6 | 4.2% | coding (1379/1782 nt) | gcl | glyoxylate carboligase |
| ? | NC_000913 | 535390 = | 136 (1.470) | coding (1475/1782 nt) | gcl | glyoxylate carboligase | |||||
| * | ? | NC_000913 | 520304 = | 64 (0.660) | 4 (0.040) | 4/262 | 7.0 | 4.4% | coding (572/687 nt) | ybbA | putative ABC transporter ATP‑binding protein YbbA |
| ? | NC_000913 | = 4306175 | 113 (1.240) | coding (423/1986 nt) | yjcS | alkyl sulfatase | |||||
| * | ? | NC_000913 | 4318188 = | 90 (0.930) | 4 (0.040) | 4/266 | 7.1 | 4.6% | coding (577/759 nt) | phnK | carbon‑phosphorus lyase subunit PhnK |
| ? | NC_000913 | = 4318184 | 80 (0.860) | coding (581/759 nt) | phnK | carbon‑phosphorus lyase subunit PhnK | |||||
| * | ? | NC_000913 | = 2809147 | 123 (1.270) | 4 (0.040) | 4/274 | 7.2 | 3.2% | pseudogene (832/1178 nt) | ygaY | putative transporter YgaY, N‑terminal fragment |
| ? | NC_000913 | 2809151 = | 124 (1.300) | pseudogene (836/1178 nt) | ygaY | putative transporter YgaY, N‑terminal fragment | |||||
| * | ? | NC_000913 | 4180665 = | 103 (1.060) | 3 (0.030) | 3/258 | 7.5 | 3.0% | coding (106/366 nt) | rplL | 50S ribosomal subunit protein L12 |
| ? | NC_000913 | = 4180661 | 100 (1.110) | coding (102/366 nt) | rplL | 50S ribosomal subunit protein L12 | |||||
| * | ? | NC_000913 | 4545168 = | 91 (0.940) | 3 (0.030) | 3/270 | 7.6 | 2.5% | coding (73/2637 nt) | fimD | type I fimbriae usher protein |
| ? | NC_000913 | = 4546624 | 141 (1.500) | coding (1529/2637 nt) | fimD | type I fimbriae usher protein | |||||