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_3_vch_tpiA | 4,296,090 | 0 | C | T | 30.7% | 83.3 / 50.5 | 76 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_vch_tpiA | 3,288,033 | 0 | T | G | 20.0% | 63.5 / 10.1 | 30 | intergenic (+23/‑57) | yraH/yraI | putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone |
| Marginal new junction evidence (lowest skew 10 of 67 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_tpiA | 1207790 = | 36 (1.270) | 6 (0.240) | 5/252 | 2.8 | 17.4% | noncoding (11571/15193 nt) | cryptic prophage e14 | cryptic prophage e14 |
| ? | NC_000913_3_vch_tpiA | 1209619 = | 25 (0.990) | noncoding (13400/15193 nt) | cryptic prophage e14 | cryptic prophage e14 | |||||
| * | ? | NC_000913_3_vch_tpiA | = 1457527 | 16 (0.560) | 5 (0.190) | 5/266 | 3.0 | 23.3% | noncoding (1457527/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 1457534 | 18 (0.680) | noncoding (1457534/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 4296174 | 20 (0.710) | 7 (0.260) | 5/270 | 3.1 | 29.8% | noncoding (310/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913_3_vch_tpiA | = 4296190 | 14 (0.520) | noncoding (326/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913_3_vch_tpiA | = 4295948 | 23 (0.810) | 7 (0.260) | 5/270 | 3.1 | 28.1% | noncoding (84/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913_3_vch_tpiA | = 4296190 | 14 (0.520) | noncoding (326/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913_3_vch_tpiA | = 2593024 | NA (NA) | 5 (0.190) | 5/270 | 3.1 | NA | noncoding (47/83 nt) | REP180 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP180 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_vch_tpiA | = 2593056 | NA (NA) | noncoding (79/83 nt) | REP180 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP180 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_vch_tpiA | 3654539 = | 24 (0.850) | 4 (0.150) | 4/260 | 3.3 | 17.8% | noncoding (3654539/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 3654568 = | 15 (0.580) | noncoding (3654568/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | 1911650 = | 38 (1.340) | 4 (0.150) | 4/260 | 3.3 | 10.4% | noncoding (1911650/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 1911680 = | 34 (1.310) | noncoding (1911680/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | 1697230 = | 24 (0.850) | 4 (0.150) | 4/260 | 3.3 | 14.6% | noncoding (1697230/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 1697261 = | 25 (0.960) | noncoding (1697261/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | 4216466 = | 38 (1.340) | 4 (0.150) | 4/268 | 3.4 | 10.4% | noncoding (4216466/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 4216509 = | 33 (1.230) | noncoding (4216509/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 4150443 | 23 (0.810) | 4 (0.150) | 4/266 | 3.4 | 15.5% | noncoding (4150443/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 4150453 | 22 (0.830) | noncoding (4150453/4641682 nt) | repeat_region | repeat region | |||||