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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 51.5% | 6.2 / 253.1 | 171 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 40.5% | 84.5 / 122.9 | 111 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 38.0% | 137.3 / 119.4 | 109 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 109 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 4399 | 1 (0.460) | 20 (0.010) | 13/244 | 0.1 | 1.6% | intergenic (+364/‑101) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1963 | 2526 (0.940) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4311 = | 0 (0.000) | 35 (0.030) | 13/244 | 0.1 | 2.5% | intergenic (+276/‑189) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2053 = | 2690 (1.000) | intergenic (+286/+40) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4294 = | 0 (0.000) | 9 (0.010) | 5/250 | 0.1 | 0.69% | intergenic (+259/‑206) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2073 = | 2588 (0.940) | intergenic (+306/+20) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 2326 | 3 (1.380) | 76 (0.050) | 17/254 | 0.1 | 5.1% | intergenic (+106/+62) | USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1986 | 2830 (1.010) | intergenic (+219/+107) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 329202 = | 129 (1.360) | 7 (0.080) | 6/246 | 10.1 | 5.9% | intergenic (+70/+73) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| ? | USA300TCH1516_ALE | 329255 = | 103 (1.180) | intergenic (+123/+20) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 | |||||
| * | ? | NC_012417 | 987 = | 3332 (1.130) | 54 (0.020) | 28/244 | 10.1 | 1.8% | pseudogene (708/709 nt) | USA300HOU_RS14890 | replication protein |
| ? | NC_012417 | 1013 = | 2873 (1.060) | coding (182/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 515519 | NA (NA) | 7 (0.080) | 6/256 | 10.4 | NA | intergenic (+3587/‑3176) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 515584 | NA (NA) | intergenic (+3652/‑3111) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | = 1873423 | 72 (0.760) | 6 (0.070) | 5/240 | 10.5 | 9.3% | intergenic (‑99/+651) | USA300HOU_RS09300/USA300HOU_RS09305 | Putative dipeptidase/hypothetical protein |
| ? | USA300TCH1516_ALE | = 1873461 | 52 (0.610) | intergenic (‑137/+613) | USA300HOU_RS09300/USA300HOU_RS09305 | Putative dipeptidase/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1759680 | 76 (0.800) | 5 (0.060) | 5/238 | 10.5 | 6.4% | intergenic (‑387/+87) | USA300HOU_RS08780/USA300HOU_RS08785 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 1759708 | 78 (0.920) | intergenic (‑415/+59) | USA300HOU_RS08780/USA300HOU_RS08785 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2492466 = | 95 (1.000) | 5 (0.060) | 5/244 | 10.6 | 5.8% | intergenic (+9/+37) | yhfP/rimI_4 | Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase |
| ? | USA300TCH1516_ALE | 2492499 = | 76 (0.880) | intergenic (+42/+4) | yhfP/rimI_4 | Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase | |||||