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 | 48.4% | 17.9 / 151.6 | 122 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 33.0% | 116.4 / 87.3 | 100 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 31.9% | 123.7 / 77.4 | 95 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,435,065 | 0 | C | G | 23.3% | 179.9 / 13.0 | 73 | A141G (GCT→GGT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,063 | 0 | T | C | 23.2% | 129.1 / 14.4 | 72 | R140R (CGT→CGC) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,081 | 0 | T | A | 20.0% | 170.1 / 17.2 | 76 | N146K (AAT→AAA) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 1912410 | 54 (0.690) | 4 (0.050) | 4/268 | 8.6 | 7.2% | coding (532/609 nt) | USA300HOU_RS15290 | hypothetical protein |
| ? | USA300TCH1516_ALE | = 2319335 | NA (NA) | coding (253/345 nt) | USA300HOU_RS15290 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1442900 = | NA (NA) | 4 (0.050) | 4/268 | 8.6 | NA | intergenic (+133/+135) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1442915 = | NA (NA) | intergenic (+148/+120) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1427028 | 41 (0.520) | 4 (0.050) | 4/268 | 8.6 | 9.3% | intergenic (‑759/+213) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B |
| ? | USA300TCH1516_ALE | 1442915 = | NA (NA) | intergenic (+148/+120) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein | |||||
| * | ? | CP000731 | 21020 = | 135 (0.240) | 5 (0.020) | 4/268 | 8.6 | 4.5% | coding (51/675 nt) | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| ? | USA300TCH1516_ALE | = 76268 | 85 (1.130) | coding (54/246 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | CP000731 | 21020 = | 135 (0.240) | 5 (0.020) | 4/268 | 8.6 | 4.9% | coding (51/675 nt) | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| ? | USA300TCH1516_ALE | 36498 = | 63 (0.840) | coding (54/675 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2681424 | 107 (1.360) | 3 (0.040) | 3/250 | 8.8 | 3.0% | intergenic (‑459/+120) | USA300HOU_RS13810/mvaA | hypothetical protein/3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase |
| ? | USA300TCH1516_ALE | = 2681449 | 98 (1.400) | intergenic (‑484/+95) | USA300HOU_RS13810/mvaA | hypothetical protein/3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase | |||||
| * | ? | USA300TCH1516_ALE | 1442915 = | NA (NA) | 4 (0.050) | 3/268 | 9.3 | 5.9% | intergenic (+148/+120) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1803138 = | 67 (0.850) | coding (730/807 nt) | USA300HOU_RS12765 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1427019 | 55 (0.700) | 4 (0.050) | 3/268 | 9.3 | 7.0% | intergenic (‑750/+222) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B |
| ? | USA300TCH1516_ALE | = 1912404 | 53 (0.710) | coding (526/609 nt) | USA300HOU_RS15290 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1427019 | 55 (0.700) | 4 (0.050) | 3/268 | 9.3 | 7.1% | intergenic (‑750/+222) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B |
| ? | USA300TCH1516_ALE | 1442906 = | NA (NA) | intergenic (+139/+129) | USA300HOU_RS07165/USA300TCH1516_01342 | TelA‑like protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1427019 | 55 (0.700) | 4 (0.050) | 3/268 | 9.3 | 8.0% | intergenic (‑750/+222) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B |
| ? | USA300TCH1516_ALE | = 1427022 | 39 (0.520) | intergenic (‑753/+219) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B | |||||