mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 62 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,861 | 0 | T | C | 76.7% | 956.6 / 250.2 | 496 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 76.5% | 844.5 / 316.1 | 498 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 75.9% | 978.9 / 263.8 | 501 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 75.9% | 823.8 / 304.7 | 500 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 75.9% | 1141.6 / inf | 503 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 75.9% | 782.8 / inf | 500 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 75.7% | 789.8 / inf | 500 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 75.7% | 1054.2 / 258.3 | 503 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 74.7% | 1108.2 / inf | 502 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,866 | 0 | G | T | 74.2% | 678.5 / inf | 500 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,876 | 0 | C | T | 71.0% | 171.8 / 261.3 | 373 | intergenic (+107/+1) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 35,858 | 0 | T | A | 68.3% | 6.7 / 176.9 | 204 | intergenic (+89/+19) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 1,929,812 | 0 | G | A | 67.4% | 359.9 / 310.5 | 355 | intergenic (‑895/‑273) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,918 | 0 | A | G | 67.1% | 507.3 / 309.0 | 396 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,917 | 0 | C | T | 66.8% | 412.4 / inf | 396 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,930 | 0 | T | A | 66.4% | 391.6 / inf | 344 | intergenic (‑1013/‑155) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,928 | 0 | T | A | 66.2% | 355.1 / inf | 344 | intergenic (‑1011/‑157) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,850 | 0 | C | T | 66.2% | ‑0.6 / 173.1 | 201 | intergenic (+81/+27) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 2,119,528 | 0 | C | T | 65.8% | 75.5 / 58.6 | 76 | D240N (GAT→AAT) | USA300HOU_1992 | hypothetical protein |
| * | CP000730 | 1,929,925 | 0 | T | A | 65.5% | 380.0 / inf | 344 | intergenic (‑1008/‑160) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 842904 = | 99 (0.920) | 4 (0.050) +29 bp |
3/222 | 12.0 | 4.5% | intergenic (+290/‑372) | uvrA/hprK | excision endonuclease subunit UvrA/HPr kinase |
| ? | CP000730 | 2220661 = | 118 (1.100) | intergenic (‑312/+250) | USA300HOU_2091/atpC | hypothetical protein/F‑ATPase superfamily proton(H+)‑ or sodium (Na+)‑translocating F‑type ATPase epsilon subunit | |||||
| * | ? | CP000730 | 36133 = | 1750 (16.270) | 6 (0.060) | 5/268 | 12.1 | 0.35% | coding (419/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | 36148 = | 1707 (16.590) | coding (404/675 nt) | tpn | IS431mec transposase | |||||
| * | ? | CP000730 | = 2136880 | 74 (0.690) | 4 (0.040) | 4/256 | 12.4 | 5.6% | intergenic (+66/+787) | USA300HOU_2018/USA300HOU_2019 | Trk family potassium (K+) transporter, ABC protein/GNAT family acetyltransferase |
| ? | CP000730 | = 2136884 | 66 (0.670) | intergenic (+70/+783) | USA300HOU_2018/USA300HOU_2019 | Trk family potassium (K+) transporter, ABC protein/GNAT family acetyltransferase | |||||
| * | ? | CP000730 | 36142 = | 1802 (16.750) | 6 (0.060) | 4/268 | 12.8 | 0.66% | coding (410/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | = 76626 | 91 (0.880) | intergenic (+684/‑450) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||
| * | ? | CP000730 | = 2551423 | 95 (0.880) | 3 (0.030) | 3/250 | 13.0 | 3.7% | intergenic (‑367/+85) | bioD/USA300HOU_2412 | dethiobiotin synthase/ABC superfamily ATP binding cassette transporter, ABC/membrane protein |
| ? | CP000730 | = 2555628 | 71 (0.740) | coding (3/108 nt) | USA300HOU_2414 | hypothetical protein | |||||
| * | ? | CP000730 | 52489 = | 100 (0.930) | 27 (0.280) | 3/250 | 13.0 | 24.2% | intergenic (+99/‑574) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52983 | 80 (0.830) | intergenic (+593/‑80) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 52495 = | 95 (0.880) | 133 (1.250) +T |
4/278 | 13.1 | 60.0% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 84 (0.780) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | = 36462 | 478 (4.440) | 4 (0.040) | 3/254 | 13.1 | 0.65% | coding (90/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | 76234 = | 795 (8.150) | intergenic (+292/‑842) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||
| * | ? | CP000730 | 836385 = | 110 (1.020) | 3 (0.030) | 3/260 | 13.3 | 2.8% | coding (776/840 nt) | USA300HOU_0783 | possible LysM family autolysin |
| ? | CP000730 | 836427 = | 104 (1.040) | coding (818/840 nt) | USA300HOU_0783 | possible LysM family autolysin | |||||
| * | ? | CP000730 | = 614093 | 161 (1.500) | 5 (0.050) | 3/258 | 13.3 | 3.4% | coding (2405/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | 622296 = | 134 (1.350) | coding (2859/3465 nt) | sdrE | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrE | |||||