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 | 58.2% | 52.2 / 124.5 | 110 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 31.4% | 95.7 / 54.3 | 70 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,435,065 | 0 | C | G | 31.1% | 90.3 / 10.2 | 45 | A141G (GCT→GGT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 31.0% | 88.2 / 59.4 | 71 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 52495 = | 56 (1.010) | 79 (1.430) +T |
5/294 | 5.9 | 57.4% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 62 (1.110) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 891951 | 60 (1.080) | 3 (0.060) | 3/282 | 6.8 | 5.0% | intergenic (+369/‑370) | USA300HOU_RS04385/rnmV_2 | hypothetical protein/Ribonuclease M5 |
| ? | USA300TCH1516_ALE | = 891954 | 56 (1.060) | intergenic (+372/‑367) | USA300HOU_RS04385/rnmV_2 | hypothetical protein/Ribonuclease M5 | |||||
| * | ? | CP000731 | = 4399 | 332 (1.190) | 7 (0.010) | 4/274 | 29.8 | 0.98% | intergenic (+364/‑101) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1963 | 1112 (1.020) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 2352 | 341 (1.230) | 7 (0.010) | 4/274 | 29.8 | 0.97% | intergenic (+132/+36) | USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1963 | 1112 (1.020) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 537 | 308 (1.110) | 3 (0.010) | 3/282 | 31.4 | 1.1% | coding (306/984 nt) | repA | replication protein A |
| ? | CP000731 | = 539 | 268 (1.010) | coding (308/984 nt) | repA | replication protein A | |||||
| * | ? | NC_012417 | = 2937 | 1321 (1.120) | 8 (0.010) | 7/286 | 68.3 | 0.64% | intergenic (‑263/–) | USA300HOU_RS14900/– | hypothetical protein/– |
| ? | NC_012417 | = 2949 | 1222 (1.070) | intergenic (‑275/–) | USA300HOU_RS14900/– | hypothetical protein/– | |||||
| * | ? | NC_012417 | = 1974 | 1209 (1.020) | 7 (0.010) | 5/274 | 69.1 | 0.63% | intergenic (+207/+119) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 2041 | 1075 (0.980) | intergenic (+274/+52) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_012417 | = 1177 | 1163 (0.980) | 5 (0.000) | 4/284 | 71.7 | 0.45% | coding (18/192 nt) | USA300HOU_RS15665 | hypothetical protein |
| ? | NC_012417 | = 1180 | 1104 (0.970) | coding (15/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||