mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 51.6% | 21.9 / inf | 244 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 35.2% | 180.5 / 141.9 | 160 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 33.3% | 187.0 / 145.3 | 165 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,435,065 | 0 | C | G | 20.0% | 200.2 / 10.9 | 76 | A141G (GCT→GGT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 800928 | 93 (0.910) | 5 (0.050) | 5/282 | 7.6 | 5.2% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 92 (0.940) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | = 517640 | NA (NA) | 6 (0.060) | 5/284 | 7.7 | NA | intergenic (+5708/‑1055) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 517643 | NA (NA) | intergenic (+5711/‑1052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 48945 = | 139 (1.350) | 6 (0.060) | 5/294 | 7.8 | 4.0% | intergenic (‑54/+180) | hin_2/USA300HOU_RS00205 | DNA‑invertase hin/hypothetical protein |
| ? | USA300TCH1516_ALE | 48974 = | 151 (1.480) | intergenic (‑83/+151) | hin_2/USA300HOU_RS00205 | DNA‑invertase hin/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 715316 | 107 (1.040) | 4 (0.040) | 4/268 | 7.9 | 3.9% | intergenic (+74/+43) | tarD/dacA | Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA |
| ? | USA300TCH1516_ALE | = 715335 | 103 (1.110) | intergenic (+93/+24) | tarD/dacA | Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA | |||||
| * | ? | USA300TCH1516_ALE | 1606572 = | 93 (0.910) | 4 (0.040) | 4/282 | 8.1 | 4.1% | coding (511/1155 nt) | USA300TCH1516_01489 | hypothetical protein |
| ? | USA300TCH1516_ALE | 1606595 = | 99 (1.010) | coding (488/1155 nt) | USA300TCH1516_01489 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1892452 | 88 (0.860) | 4 (0.040) | 3/278 | 8.6 | 4.6% | coding (200/225 nt) | USA300TCH1516_01749 | hypothetical protein |
| ? | USA300TCH1516_ALE | = 1892462 | 83 (0.860) | coding (190/225 nt) | USA300TCH1516_01749 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2328479 = | 128 (1.250) | 4 (0.040) | 3/288 | 8.8 | 3.2% | coding (1185/1713 nt) | lacE | PTS system lactose‑specific EIICB component |
| ? | USA300TCH1516_ALE | 2328561 = | 118 (1.180) | coding (1103/1713 nt) | lacE | PTS system lactose‑specific EIICB component | |||||
| * | ? | CP000731 | = 4433 | 529 (1.070) | 91 (0.110) +46 bp |
3/204 | 42.0 | 9.8% | intergenic (+398/‑67) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 2166 | 1912 (0.990) | coding (509/582 nt) | USA300HOU_RS14900 | hypothetical protein | |||||
| * | ? | CP000731 | = 2326 | 555 (1.130) | 21 (0.020) | 9/284 | 44.3 | 1.5% | intergenic (+106/+62) | USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1986 | 2208 (1.190) | intergenic (+219/+107) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4294 = | 548 (1.110) | 10 (0.010) | 8/280 | 44.8 | 0.86% | intergenic (+259/‑206) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2073 = | 1800 (0.980) | intergenic (+306/+20) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||