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 | 55.3% | 138.3 / inf | 402 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 30.7% | 362.8 / 206.6 | 257 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 30.4% | 376.4 / 173.0 | 231 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 1623 | 1236 (0.920) | 11 (0.020) | 6/272 | 0.8 | 1.9% | intergenic (+408/‑448) | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| ? | NC_012417 | = 1066 | 15 (0.840) | coding (129/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | CP000731 | 1596 = | 1155 (0.860) | 5 (0.010) | 4/288 | 1.5 | 0.86% | intergenic (+381/‑475) | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| ? | NC_012417 | 1127 = | 25 (1.320) | coding (68/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 68659 = | 131 (0.700) | 11 (0.070) | 11/260 | 12.3 | 8.7% | coding (775/852 nt) | USA300TCH1516_00061 | hypothetical protein |
| ? | USA300TCH1516_ALE | = 68655 | 115 (0.700) | coding (771/852 nt) | USA300TCH1516_00061 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 139 (0.740) | 218 (1.180) +T |
8/294 | 15.3 | 63.2% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 117 (0.630) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 52489 = | 146 (0.780) | 32 (0.190) | 6/266 | 15.5 | 21.0% | intergenic (+99/‑574) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52983 | 110 (0.660) | intergenic (+593/‑80) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 705321 = | 185 (0.990) | 5 (0.030) | 5/278 | 16.8 | 2.7% | intergenic (+1071/+89) | nhaK_1/mntA | Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA |
| ? | USA300TCH1516_ALE | 705378 = | 186 (1.060) | intergenic (+1128/+32) | nhaK_1/mntA | Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 210 (1.120) | 6 (0.030) | 5/282 | 16.9 | 3.1% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 181 (1.020) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | CP000731 | 21011 = | 313 (0.230) | 6 (0.010) | 5/284 | 17.0 | 2.4% | coding (60/675 nt) | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| ? | USA300TCH1516_ALE | = 76259 | 182 (1.020) | coding (45/246 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | CP000731 | 17002 = | 347 (0.260) | 8 (0.010) | 5/284 | 17.0 | 3.0% | coding (60/675 nt) | USA300HOU_pUSA300HOUMR0021 | IS431 mec transposase |
| ? | USA300TCH1516_ALE | = 76259 | 182 (1.020) | coding (45/246 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 177 (0.950) | 39 (0.210) | 5/296 | 17.5 | 18.1% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1205383 = | 175 (0.940) | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase | |||||