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 | 1,544,021 | 1 | . | A | 73.1% | 52.4 / 20.2 | 26 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| * | NC_000913_3_vch_tpiA | 4,159,190 | 0 | T | A | 68.8% | 42.7 / 17.9 | 32 | L224Q (CTG→CAG) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_vch_tpiA | 4,296,090 | 0 | C | T | 24.6% | 69.4 / 30.5 | 57 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_vch_tpiA | 4,159,007 | 0 | A | C | 24.3% | 42.1 / 14.7 | 38 | E163A (GAG→GCG) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 60 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_tpiA | 1207790 = | 24 (0.740) | 6 (0.210) | 6/250 | 3.0 | 20.6% | noncoding (11571/15193 nt) | cryptic prophage e14 | cryptic prophage e14 |
| ? | NC_000913_3_vch_tpiA | 1209619 = | 25 (0.870) | noncoding (13400/15193 nt) | cryptic prophage e14 | cryptic prophage e14 | |||||
| * | ? | NC_000913_3_vch_tpiA | 2118491 = | NA (NA) | 7 (0.230) | 6/268 | 3.2 | 17.1% | noncoding (26/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_vch_tpiA | 3708329 = | 34 (1.110) | noncoding (58/86 nt) | REP267 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP267 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_vch_tpiA | 59280 = | 35 (1.080) | 9 (0.320) | 5/248 | 3.3 | 24.1% | noncoding (59280/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 59320 = | 26 (0.920) | noncoding (59320/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 2603295 | 26 (0.800) | 5 (0.160) | 5/268 | 3.6 | 17.3% | noncoding (2603295/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 2603299 | 23 (0.750) | noncoding (2603299/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | 2118491 = | NA (NA) | 5 (0.160) | 5/268 | 3.6 | NA | noncoding (26/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_vch_tpiA | 4245170 = | NA (NA) | noncoding (49/126 nt) | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913_3_vch_tpiA | 2118491 = | NA (NA) | 5 (0.160) | 5/268 | 3.6 | 11.1% | noncoding (26/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_vch_tpiA | 2118569 = | 40 (1.300) | noncoding (104/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913_3_vch_tpiA | 2118466 = | NA (NA) | 5 (0.160) | 5/268 | 3.6 | NA | noncoding (1/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_vch_tpiA | 2118498 = | NA (NA) | noncoding (33/186 nt) | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913_3_vch_tpiA | = 1097463 | 10 (0.310) | 5 (0.160) | 5/266 | 3.6 | 35.2% | noncoding (1097463/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 1097467 | 9 (0.300) | noncoding (1097467/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 1097294 | 14 (0.430) | 5 (0.160) | 5/266 | 3.6 | 32.0% | noncoding (1097294/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 1097455 | 8 (0.260) | noncoding (1097455/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 1097113 | 26 (0.800) | 5 (0.160) | 5/266 | 3.6 | 23.5% | noncoding (1097113/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | = 1097455 | 8 (0.260) | noncoding (1097455/4641682 nt) | repeat_region | repeat region | |||||