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_hsa_tpiA | 3,657,599 | 0 | T | A | 25.0% | 41.4 / 14.8 | 24 | intergenic (+32/+387) | hdeD/arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| * | NC_000913_3_hsa_tpiA | 3,657,601 | 0 | G | C | 25.0% | 37.3 / 16.1 | 25 | intergenic (+34/+385) | hdeD/arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| * | NC_000913_3_hsa_tpiA | 3,657,603 | 0 | T | A | 25.0% | 43.3 / 12.8 | 24 | intergenic (+36/+383) | hdeD/arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| * | NC_000913_3_hsa_tpiA | 1,642,370 | 0 | C | G | 20.0% | 36.2 / 11.4 | 25 | intergenic (+303/+119) | cspF/quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| * | NC_000913_3_hsa_tpiA | 1,642,373 | 0 | C | G | 20.0% | 52.4 / 11.3 | 25 | intergenic (+306/+116) | cspF/quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | = 4094510 | 63 (2.570) | 4 (0.170) | 4/270 | 2.8 | 5.4% | noncoding (195/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913_3_hsa_tpiA | = 4094618 | 79 (3.390) | noncoding (303/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3363806 = | 29 (1.180) | 4 (0.170) | 4/272 | 2.8 | 13.0% | coding (1000/2382 nt) | yhcD | putative outer membrane fimbrial subunit usher protein |
| ? | NC_000913_3_hsa_tpiA | 3363821 = | 26 (1.110) | coding (1015/2382 nt) | yhcD | putative outer membrane fimbrial subunit usher protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3159421 | 18 (0.730) | 4 (0.170) | 4/272 | 2.8 | 17.7% | coding (1726/2220 nt) | ygiQ | Radical SAM superfamily protein |
| ? | NC_000913_3_hsa_tpiA | = 3159442 | 20 (0.850) | coding (1705/2220 nt) | ygiQ | Radical SAM superfamily protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1226143 | 19 (0.770) | 4 (0.170) | 4/266 | 2.8 | 17.5% | intergenic (‑63/‑457) | minC/ycgJ | inhibitor of FtsZ ring polymerization/uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1226149 | 20 (0.870) | intergenic (‑69/‑451) | minC/ycgJ | inhibitor of FtsZ ring polymerization/uncharacterized protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4040683 | 42 (1.710) | 7 (0.290) | 4/280 | 2.9 | 18.3% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913_3_hsa_tpiA | = 4213144 | 21 (0.870) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1552279 = | NA (NA) | 3 (0.130) | 3/260 | 3.1 | NA | noncoding (31/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_hsa_tpiA | 4080020 = | NA (NA) | noncoding (1/98 nt) | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1552101 = | NA (NA) | 3 (0.130) | 3/260 | 3.1 | NA | noncoding (31/97 nt) | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_hsa_tpiA | 4080020 = | NA (NA) | noncoding (1/98 nt) | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP297 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4347357 | 18 (0.730) | 3 (0.130) | 3/266 | 3.2 | 14.0% | intergenic (‑49/+29) | fumB/dcuB | anaerobic class I fumarate hydratase (fumarase B)/C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor |
| ? | NC_000913_3_hsa_tpiA | = 4347367 | 20 (0.870) | intergenic (‑59/+19) | fumB/dcuB | anaerobic class I fumarate hydratase (fumarase B)/C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3723012 | 19 (0.770) | 3 (0.130) | 3/270 | 3.2 | 13.9% | coding (1386/2070 nt) | glyS | glycine tRNA synthetase, beta subunit |
| ? | NC_000913_3_hsa_tpiA | = 3723016 | 19 (0.810) | coding (1382/2070 nt) | glyS | glycine tRNA synthetase, beta subunit | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 213451 | 30 (1.220) | 3 (0.130) | 3/270 | 3.2 | 9.9% | coding (1121/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase |
| ? | NC_000913_3_hsa_tpiA | = 213488 | 26 (1.110) | coding (1158/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase | |||||