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_pgi | 526,792 | 0 | A | C | 40.4% | 30.9 / 46.6 | 50 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 40.4% | 34.6 / 43.4 | 47 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 40.0% | 53.2 / 52.5 | 50 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 964,150 | 0 | T | A | 26.3% | 27.6 / 11.4 | 19 | intergenic (+38/‑170) | ihfB/ycaI | integration host factor (IHF), DNA‑binding protein, beta subunit/ComEC family inner membrane protein |
| * | NC_000913_3_pae_pgi | 3,708,427 | 0 | G | A | 22.6% | 51.8 / 10.3 | 31 | intergenic (‑722/+189) | dppA/proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| * | NC_000913_3_pae_pgi | 3,708,428 | 0 | T | A | 22.6% | 51.7 / 14.3 | 31 | intergenic (‑723/+188) | dppA/proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| * | NC_000913_3_pae_pgi | 3,708,429 | 0 | T | C | 22.6% | 48.8 / 13.0 | 31 | intergenic (‑724/+187) | dppA/proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| * | NC_000913_3_pae_pgi | 3,891,506 | 0 | C | G | 21.4% | 56.6 / 11.8 | 29 | intergenic (+23/‑109) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| Marginal new junction evidence (lowest skew 10 of 63 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 2304653 | 32 (1.190) | 5 (0.200) | 5/268 | 2.8 | 18.1% | noncoding (237/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913_3_pae_pgi | = 2304895 | 15 (0.590) | noncoding (479/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | 951204 = | 31 (1.150) | 5 (0.190) | 5/278 | 2.9 | 13.4% | intergenic (‑124/+68) | pflA/pflB | pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase/formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| ? | NC_000913_3_pae_pgi | 951236 = | 34 (1.280) | intergenic (‑156/+36) | pflA/pflB | pyruvate formate‑lyase 1‑activating enzyme; [formate‑C‑acetyltransferase 1]‑activating enzyme; PFL activase/formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 | |||||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 19 (0.700) | 4 (0.170) | 4/250 | 3.0 | 17.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 21 (0.880) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | = 1863799 | 31 (1.150) | 4 (0.160) | 4/258 | 3.1 | 12.1% | intergenic (+33/‑51) | gapA/yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| ? | NC_000913_3_pae_pgi | = 1863803 | 30 (1.220) | intergenic (+37/‑47) | gapA/yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 4295553 | 0 (0.000) | 4 (0.160) | 4/268 | 3.2 | 50.0% | noncoding (459/600 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_pgi | = 4295572 | 8 (0.310) | noncoding (478/600 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_pgi | = 4295466 | 0 (0.000) | 4 (0.160) | 4/268 | 3.2 | 100% | noncoding (372/600 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_pgi | = 4295546 | 0 (0.000) | noncoding (452/600 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_pgi | = 4295440 | 6 (0.220) | 4 (0.160) | 4/268 | 3.2 | 36.9% | noncoding (346/600 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_pgi | = 4295572 | 8 (0.310) | noncoding (478/600 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_pgi | = 4295440 | 6 (0.220) | 4 (0.160) | 4/268 | 3.2 | 58.4% | noncoding (346/600 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_pgi | = 4295459 | 0 (0.000) | noncoding (365/600 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_pgi | = 4295240 | 36 (1.330) | 4 (0.160) | 4/268 | 3.2 | 18.9% | noncoding (146/600 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_pgi | = 4295546 | 0 (0.000) | noncoding (452/600 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_pgi | = 4295240 | 36 (1.330) | 4 (0.160) | 4/268 | 3.2 | 16.6% | noncoding (146/600 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_pgi | = 4295433 | 6 (0.230) | noncoding (339/600 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 | |||||