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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,825,061 | 0 | G | A | 39.0% | 53.4 / 17.9 | 41 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.5% | 143.9 / 66.1 | 115 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 101.8 / 41.8 | 72 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.9% | 127.7 / 35.6 | 79 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.6% | 196.6 / 120.5 | 138 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 445,558 | 0 | A | C | 30.2% | 102.6 / 32.3 | 63 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 753,125 | 0 | T | A | 30.2% | 119.6 / 21.3 | 63 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.2% | 154.6 / 34.7 | 63 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 28.4% | 135.0 / 24.6 | 74 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,206,446 | 0 | C | A | 27.4% | 157.1 / 14.2 | 73 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.0% | 258.6 / 14.8 | 129 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,101,507 | 0 | T | G | 26.8% | 137.5 / 14.2 | 71 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 26.2% | 119.0 / 31.6 | 65 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,525 | 0 | C | T | 25.7% | 148.8 / 13.4 | 70 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 25.0% | 118.6 / 12.5 | 60 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,377,140 | 0 | A | C | 24.1% | 164.9 / 12.4 | 83 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 2,628,625 | 0 | A | C | 23.4% | 142.4 / 10.3 | 64 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,240,985 | 0 | T | G | 22.7% | 159.9 / 18.7 | 75 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 3,556,205 | 0 | A | C | 22.6% | 117.3 / 10.0 | 53 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.6% | 212.8 / 46.6 | 102 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 147 (1.110) | 20 (0.170) | 18/246 | 4.0 | 14.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 108 (0.920) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 84 (0.640) | 18 (0.150) | 15/260 | 4.9 | 16.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 104 (0.840) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 94 (0.710) | 17 (0.140) | 14/260 | 5.1 | 15.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 105 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979417 | 104 (0.790) | 11 (0.080) | 11/278 | 6.2 | 9.6% | intergenic (‑202/‑336) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 11 (0.080) | 11/278 | 6.2 | 9.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1979417 | 104 (0.790) | intergenic (‑202/‑336) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 12 (0.090) | 10/278 | 6.6 | 10.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979410 = | 98 (0.740) | intergenic (‑195/‑343) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 11 (0.080) | 10/278 | 6.6 | 10.1% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979410 = | 98 (0.740) | intergenic (‑195/‑343) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 290634 = | NA (NA) | 8 (0.060) | 8/278 | 7.3 | 7.5% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979410 = | 98 (0.740) | intergenic (‑195/‑343) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1049778 = | NA (NA) | 7 (0.050) | 7/276 | 7.6 | 6.3% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1979417 | 104 (0.790) | intergenic (‑202/‑336) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 1979417 | 104 (0.790) | 5 (0.040) +GGTG |
5/270 | 8.4 | 4.7% | intergenic (‑202/‑336) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 4518476 = | NA (NA) | noncoding (5/768 nt) | IS1 | repeat region | |||||