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 | 4,604,344 | 0 | C | T | 44.6% | 85.7 / 93.1 | 112 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.4% | 215.1 / 24.7 | 123 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 372,640 | 0 | T | G | 30.1% | 166.3 / 30.3 | 93 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 29.8% | 72.2 / 24.0 | 47 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 753,125 | 0 | T | A | 28.4% | 140.4 / 27.1 | 67 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.1% | 104.6 / 20.2 | 57 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,101,514 | 0 | G | T | 27.3% | 207.7 / 31.4 | 77 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.5% | 129.1 / 34.7 | 68 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 26.1% | 91.2 / 16.4 | 46 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,223,593 | 0 | T | G | 25.3% | 187.8 / 11.1 | 87 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.5% | 309.7 / 97.3 | 155 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.3% | 315.2 / 25.6 | 150 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.0% | 281.0 / 37.9 | 135 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.2% | 186.4 / 22.7 | 63 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,105 | 0 | A | T | 21.2% | 205.5 / 23.6 | 80 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 20.9% | 192.2 / 16.7 | 86 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 646,747 | 0 | T | G | 20.8% | 172.4 / 26.2 | 77 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 1,261,842 | 0 | T | G | 20.7% | 183.2 / 24.9 | 82 | T12P (ACC→CCC) | prs | ribose‑phosphate diphosphokinase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 20.7% | 265.4 / 25.5 | 121 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 753,114 | 0 | G | T | 20.6% | 181.6 / 11.7 | 68 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 39 (0.310) | 20/276 | 4.6 | 27.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1105157 = | 103 (0.820) | coding (197/333 nt) | csgC | inhibitor of CsgA amyloid formation | |||||
| * | ? | NC_000913 | = 4542690 | 84 (0.670) | 11 (0.090) | 10/258 | 6.9 | 11.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 100 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 89 (0.710) | 9 (0.080) | 9/258 | 7.3 | 8.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 101 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1105157 = | 103 (0.820) | 5 (0.040) | 5/270 | 9.3 | 4.7% | coding (197/333 nt) | csgC | inhibitor of CsgA amyloid formation |
| ? | NC_000913 | 2066159 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1049984 | NA (NA) | 3 (0.030) | 3/258 | 10.2 | 8.4% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3583540 | 35 (0.280) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1049984 | NA (NA) | 3 (0.030) | 3/258 | 10.2 | 100% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979158 = | 0 (0.000) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 291195 = | NA (NA) | 3 (0.030) | 3/258 | 10.2 | 8.4% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 291289 = | 35 (0.280) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 279724 = | NA (NA) | 3 (0.030) | 3/258 | 10.2 | 13.8% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 279818 = | 20 (0.160) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 258563 = | 0 (0.000) | 3 (0.030) | 3/258 | 10.2 | 100% | noncoding (113/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 279724 = | NA (NA) | noncoding (207/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 20451 = | 42 (0.330) | 3 (0.030) | 3/258 | 10.2 | 7.1% | noncoding (113/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 279724 = | NA (NA) | noncoding (207/768 nt) | IS1 | repeat region | |||||