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 25 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 | 46.8% | 84.3 / 97.1 | 124 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 36.4% | 66.4 / 35.1 | 55 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.4% | 153.4 / 33.0 | 86 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,101,507 | 0 | T | G | 29.3% | 196.5 / 17.9 | 99 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.9% | 115.8 / 32.6 | 67 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.5% | 244.4 / 27.3 | 94 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 25.3% | 189.0 / 20.2 | 91 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 650,809 | 0 | T | G | 25.3% | 193.2 / 27.7 | 95 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.2% | 289.3 / 94.6 | 151 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 25.0% | 154.7 / 31.6 | 76 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 29,496 | 0 | T | A | 24.7% | 185.8 / 30.3 | 81 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 24.5% | 312.6 / 17.2 | 149 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.3% | 186.8 / 31.9 | 70 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 23.9% | 143.8 / 17.5 | 67 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,752 | 0 | T | C | 22.6% | 201.0 / 10.7 | 93 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.4% | 214.3 / 42.8 | 98 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 22.4% | 156.6 / 15.1 | 67 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 21.9% | 179.5 / 12.2 | 82 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.9% | 226.9 / 20.9 | 105 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 3,556,207 | 0 | T | C | 21.9% | 139.5 / 14.1 | 64 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 175 (1.210) | 29 (0.230) | 21/246 | 4.0 | 17.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 114 (0.890) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 98 (0.680) | 26 (0.190) | 22/260 | 4.1 | 18.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 139 (1.030) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 162 (1.120) | 28 (0.220) | 19/246 | 4.4 | 18.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 112 (0.870) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 103 (0.710) | 15 (0.110) | 14/260 | 5.9 | 11.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 139 (1.030) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979413 = | 145 (1.000) | 8 (0.060) | 6/278 | 9.1 | 5.2% | intergenic (‑198/‑340) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4096897 = | 174 (1.200) | 6 (0.040) | 4/258 | 9.8 | 3.6% | coding (552/1470 nt) | rhaB | rhamnulokinase |
| ? | NC_000913 | 4097035 = | 156 (1.160) | coding (414/1470 nt) | rhaB | rhamnulokinase | |||||
| * | ? | NC_000913 | = 3468340 | 166 (1.140) | 4 (0.030) | 4/262 | 9.8 | 2.4% | coding (1514/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | = 3468506 | 167 (1.220) | coding (1348/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 701376 | 130 (0.900) | 4 (0.030) | 4/258 | 9.8 | 3.2% | coding (219/1221 nt) | nagC | DNA‑binding transcriptional dual regulator NagC |
| ? | NC_000913 | = 701527 | 119 (0.880) | coding (68/1221 nt) | nagC | DNA‑binding transcriptional dual regulator NagC | |||||
| * | ? | NC_000913 | 3943844 = | NA (NA) | 4 (0.030) | 4/266 | 9.9 | 4.6% | noncoding (141/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | 3943897 = | 87 (0.600) | noncoding (194/2904 nt) | rrlC | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 535294 = | 178 (1.230) | 6 (0.040) | 4/266 | 9.9 | 3.7% | coding (1379/1782 nt) | gcl | glyoxylate carboligase |
| ? | NC_000913 | 535390 = | 143 (1.030) | coding (1475/1782 nt) | gcl | glyoxylate carboligase | |||||