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_pae_tpiA | 4,295,976 | 0 | C | T | 25.0% | 138.8 / 43.1 | 89 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 1 | . | A | 20.0% | 115.4 / 36.9 | 45 | coding (39/1389 nt) | narU | nitrate/nitrite transporter |
| Marginal new junction evidence (lowest skew 10 of 216 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 1207805 | 39 (0.740) | 13 (0.280) | 13/252 | 3.4 | 25.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | = 1209602 | 41 (0.870) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 349969 | NA (NA) | 6 (0.190) +59 bp |
4/166 | 4.8 | NA | noncoding (365/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913_3_pae_tpiA | = 349972 | NA (NA) | intergenic (+400/‑40) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 349876 | 59 (1.110) | 6 (0.190) +59 bp |
4/166 | 4.8 | 14.8% | noncoding (272/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913_3_pae_tpiA | = 349972 | NA (NA) | intergenic (+400/‑40) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 349783 | 54 (1.020) | 6 (0.190) +59 bp |
4/166 | 4.8 | 16.0% | noncoding (179/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913_3_pae_tpiA | = 349972 | NA (NA) | intergenic (+400/‑40) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase | |||||
| * | ? | NC_000913_3_pae_tpiA | 632111 = | NA (NA) | 4 (0.120) +52 bp |
4/180 | 5.2 | NA | intergenic (+112/‑71) | cstA/ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| ? | NC_000913_3_pae_tpiA | 3676139 = | NA (NA) | noncoding (19/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3037834 | 49 (0.920) | 8 (0.160) | 8/268 | 5.4 | 14.3% | coding (273/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| ? | NC_000913_3_pae_tpiA | = 3037842 | 50 (1.000) | coding (265/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific | |||||
| * | ? | NC_000913_3_pae_tpiA | 3676121 = | NA (NA) | 7 (0.140) | 7/270 | 5.9 | NA | noncoding (1/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_tpiA | 3676146 = | NA (NA) | noncoding (26/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_tpiA | 3297032 = | NA (NA) | 7 (0.140) | 7/270 | 5.9 | NA | noncoding (34/84 nt) | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_pae_tpiA | 4295751 = | NA (NA) | noncoding (1/600 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_pae_tpiA | 3297025 = | NA (NA) | 7 (0.140) | 7/270 | 5.9 | 11.1% | noncoding (27/84 nt) | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_pae_tpiA | 4296321 = | 56 (1.110) | noncoding (571/600 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_pae_tpiA | 3296999 = | NA (NA) | 7 (0.140) | 7/270 | 5.9 | NA | noncoding (1/84 nt) | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_pae_tpiA | 3297032 = | NA (NA) | noncoding (34/84 nt) | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||