mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 1,269,785 | 0 | G | A | 44.9% | 85.4 / 128.0 | 99 | T9I (ACT→ATT) | ldrB | small toxic polypeptide LdrB |
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.6% | 78.0 / 50.2 | 77 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,764,165 | 0 | T | C | 41.2% | 45.5 / 59.6 | 51 | L661L (CTT→CTC) | rhsA | rhs element protein RhsA |
| * | NC_000913 | 3,875,653 | 0 | C | T | 40.6% | 67.0 / 109.8 | 96 | Y72Y (TAC→TAT) | yidX | putative lipoprotein YidX |
| * | NC_000913 | 4,111,747 | 0 | G | T | 38.9% | 63.8 / 20.6 | 36 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.7% | 39.3 / 12.5 | 28 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,326,450 | 0 | T | G | 31.2% | 82.8 / 23.8 | 48 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,269,897 | 0 | T | G | 30.8% | 192.5 / 142.7 | 121 | noncoding (40/66 nt) | rdlB | small regulatory antisense RNA RdlB |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.0% | 153.4 / 67.8 | 93 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.5% | 91.8 / 22.2 | 51 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.4% | 156.7 / 22.5 | 63 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,101,525 | 0 | C | T | 25.4% | 127.2 / 11.3 | 63 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.0% | 121.5 / 13.8 | 56 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,269,329 | 1 | . | T | 24.7% | 200.2 / 89.8 | 73 | noncoding (7/67 nt) | rdlA | putative antisense RNA regulator of LdrA |
| * | NC_000913 | 1,491,103 | 0 | A | C | 23.7% | 171.5 / 13.1 | 76 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,679,688 | 0 | T | G | 22.0% | 133.5 / 11.8 | 59 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| * | NC_000913 | 2,168,966 | 0 | A | C | 21.8% | 185.6 / 11.0 | 78 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 20.4% | 101.1 / 11.5 | 44 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| 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 | 1207790 = | 110 (1.360) | 16 (0.220) | 15/244 | 2.9 | 14.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 91 (1.280) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 65 (0.800) | 19 (0.250) | 15/258 | 3.1 | 22.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 67 (0.890) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 74 (0.920) | 12 (0.160) | 12/258 | 3.7 | 15.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 67 (0.890) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 93 (1.150) | 3 (0.040) | 3/244 | 6.7 | 3.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 91 (1.280) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 2683557 | 87 (1.080) | 3 (0.040) | 3/264 | 7.0 | 3.2% | coding (695/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like |
| ? | NC_000913 | = 2683637 | 99 (1.280) | coding (775/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like | |||||
| * | ? | NC_000913 | 2683552 = | 109 (1.350) | 3 (0.040) | 3/264 | 7.0 | 2.9% | coding (690/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like |
| ? | NC_000913 | 2683644 = | 99 (1.280) | coding (782/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like | |||||
| * | ? | NC_000913 | = 715737 | 86 (1.060) | 3 (0.040) | 3/262 | 7.0 | 3.7% | coding (326/495 nt) | ybfP | lipoprotein YbfP |
| ? | NC_000913 | = 715783 | 73 (0.950) | coding (372/495 nt) | ybfP | lipoprotein YbfP | |||||