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 | 2,119,528 | 0 | C | T | 66.7% | 85.8 / 59.6 | 75 | D236N (GAT→AAT) | smc_4 | Chromosome partition protein Smc |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 51.6% | 13.8 / 263.7 | 192 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 2,276,545 | 0 | C | A | 31.2% | 110.8 / 51.2 | 77 | T633K (ACA→AAA) | mtlR | Transcriptional regulator MtlR |
| * | USA300TCH1516_ALE | 2,143,110 | 0 | G | A | 28.7% | 150.9 / 73.4 | 101 | V163V (GTG→GTA) | USA300HOU_RS10935 | hypothetical protein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 23.1% | 250.8 / 70.4 | 134 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 22.6% | 265.4 / 67.9 | 135 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 2136880 | 74 (0.700) | 4 (0.040) | 4/256 | 12.4 | 5.6% | intergenic (+66/+787) | ktrB_2/ypeA_1 | Ktr system potassium uptake protein B/Acetyltransferase YpeA |
| ? | USA300TCH1516_ALE | = 2136884 | 66 (0.680) | intergenic (+70/+783) | ktrB_2/ypeA_1 | Ktr system potassium uptake protein B/Acetyltransferase YpeA | |||||
| * | ? | USA300TCH1516_ALE | 36148 = | NA (NA) | 4 (0.040) | 4/268 | 12.7 | 5.0% | coding (404/675 nt) | USA300HOU_RS00140 | hypothetical protein |
| ? | USA300TCH1516_ALE | = 76632 | 80 (0.750) | intergenic (+172/‑444) | USA300HOU_RS00140/USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase | |||||
| * | ? | USA300TCH1516_ALE | = 2551423 | 94 (0.880) | 3 (0.030) | 3/250 | 12.9 | 3.7% | intergenic (‑367/+85) | bioD1/USA300HOU_RS13150 | ATP‑dependent dethiobiotin synthetase BioD 1/putative ABC transporter ATP‑binding protein |
| ? | USA300TCH1516_ALE | = 2555628 | 71 (0.750) | intergenic (‑599/+270) | irtA/yfdG | Iron import ATP‑binding/permease protein IrtA/Prophage bactoprenol‑linked glucose translocase | |||||
| * | ? | USA300TCH1516_ALE | = 614093 | 155 (1.460) | 4 (0.040) | 3/258 | 13.2 | 2.9% | coding (2405/2844 nt) | sdrC | Serine‑aspartate repeat‑containing protein C |
| ? | USA300TCH1516_ALE | 622296 = | 129 (1.320) | coding (2859/3465 nt) | sdrE | Serine‑aspartate repeat‑containing protein E | |||||
| * | ? | USA300TCH1516_ALE | = 2622931 | 85 (0.800) | 3 (0.030) | 3/262 | 13.3 | 3.5% | intergenic (‑261/+123) | USA300HOU_RS13520/USA300TCH1516_02501 | hypothetical protein/Putative surface protein |
| ? | USA300TCH1516_ALE | = 2622960 | 88 (0.880) | intergenic (‑290/+94) | USA300HOU_RS13520/USA300TCH1516_02501 | hypothetical protein/Putative surface protein | |||||
| * | ? | USA300TCH1516_ALE | 836385 = | 110 (1.030) | 3 (0.030) | 3/260 | 13.3 | 2.8% | coding (776/840 nt) | ssaA_1 | Staphylococcal secretory antigen SsaA |
| ? | USA300TCH1516_ALE | 836427 = | 104 (1.050) | coding (818/840 nt) | ssaA_1 | Staphylococcal secretory antigen SsaA | |||||
| * | ? | USA300TCH1516_ALE | 2846891 = | 108 (1.020) | 3 (0.030) | 3/266 | 13.5 | 2.8% | intergenic (‑95/‑285) | salL/yceI | Adenosyl‑chloride synthase/Protein YceI |
| ? | USA300TCH1516_ALE | 2846923 = | 106 (1.050) | intergenic (‑127/‑253) | salL/yceI | Adenosyl‑chloride synthase/Protein YceI | |||||
| * | ? | USA300TCH1516_ALE | = 1562383 | 140 (1.320) | 3 (0.030) | 3/268 | 13.5 | 2.6% | intergenic (‑349/+41) | hlgC_1/lytN_2 | Gamma‑hemolysin component C/putative cell wall hydrolase LytN |
| ? | USA300TCH1516_ALE | = 1562397 | 90 (0.880) | intergenic (‑363/+27) | hlgC_1/lytN_2 | Gamma‑hemolysin component C/putative cell wall hydrolase LytN | |||||
| * | ? | CP000731 | 16652 = | 99 (0.140) | 4 (0.010) | 3/268 | 13.5 | 4.5% | coding (410/675 nt) | USA300HOU_pUSA300HOUMR0021 | IS431 mec transposase |
| ? | USA300TCH1516_ALE | = 76626 | 77 (0.760) | intergenic (+166/‑450) | USA300HOU_RS00140/USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 95 (0.890) | 125 (1.180) +T |
3/278 | 13.8 | 58.9% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 81 (0.760) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||