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 (highest frequency 20 of 96 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,872 | 0 | G | A | 73.7% | 462.5 / 211.8 | 309 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 73.4% | 428.6 / 231.4 | 311 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 73.3% | 583.8 / 182.9 | 311 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 72.8% | 451.9 / 229.1 | 310 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,861 | 0 | T | C | 72.8% | 536.2 / 182.2 | 310 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 72.7% | 507.1 / 201.4 | 312 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 71.2% | 582.3 / inf | 320 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 71.0% | 388.8 / 271.5 | 321 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 70.9% | 571.6 / inf | 319 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,866 | 0 | G | T | 70.5% | 358.4 / 228.9 | 311 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,812 | 0 | G | A | 66.8% | 198.1 / 190.9 | 222 | intergenic (‑895/‑273) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,744,362 | 0 | G | A | 65.8% | 47.0 / 65.5 | 76 | H104Y (CAC→TAC) | apt | adenine phosphoribosyltransferase |
| * | CP000730 | 1,233,504 | 0 | T | A | 65.1% | 62.9 / 60.7 | 65 | V470D (GTT→GAT) | prkC | non‑specific serine/threonine protein kinase |
| * | CP000730 | 1,929,918 | 0 | A | G | 64.5% | 321.0 / 221.2 | 282 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,917 | 0 | C | T | 64.2% | 272.3 / 243.3 | 282 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,928 | 0 | T | A | 62.7% | 223.4 / 254.7 | 244 | intergenic (‑1011/‑157) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,925 | 0 | T | A | 62.4% | 201.4 / 243.4 | 244 | intergenic (‑1008/‑160) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,930 | 0 | T | A | 62.3% | 211.3 / 252.3 | 244 | intergenic (‑1013/‑155) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,970 | 0 | T | C | 61.6% | 1069.0 / inf | 1404 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,269 | 0 | C | T | 61.2% | 596.3 / inf | 1709 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 2085296 = | 77 (0.810) | 11 (0.130) | 10/258 | 7.1 | 12.8% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 80 (0.930) | intergenic (+57/+1062) | int/hlgB | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | = 800928 | 82 (0.860) | 9 (0.100) | 7/272 | 8.8 | 11.1% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 66 (0.730) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | 36142 = | 1549 (16.300) | 7 (0.080) | 7/274 | 8.9 | 0.88% | coding (410/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | = 76626 | 93 (1.020) | intergenic (+684/‑450) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||
| * | ? | CP000730 | 36133 = | 1477 (15.550) | 7 (0.080) | 6/274 | 9.4 | 0.48% | coding (419/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | 36148 = | 1478 (16.240) | coding (404/675 nt) | tpn | IS431mec transposase | |||||
| * | ? | CP000730 | 52489 = | 84 (0.880) | 24 (0.280) | 5/256 | 9.5 | 24.6% | intergenic (+99/‑574) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52983 | 72 (0.850) | intergenic (+593/‑80) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 613948 = | 113 (1.190) | 9 (0.100) | 5/282 | 10.2 | 6.7% | coding (2260/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | = 614091 | 140 (1.490) | coding (2403/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC | |||||
| * | ? | CP000730 | 127971 = | 135 (1.420) | 4 (0.040) | 4/270 | 10.5 | 3.1% | intergenic (+191/+138) | lctP/spa | LctP family L‑lactate permease/immunoglobulin G binding protein A |
| ? | CP000730 | 128009 = | 122 (1.360) | intergenic (+229/+100) | lctP/spa | LctP family L‑lactate permease/immunoglobulin G binding protein A | |||||
| * | ? | CP000730 | 2661788 = | 114 (1.200) | 3 (0.040) | 3/254 | 10.8 | 3.0% | intergenic (‑181/‑140) | USA300HOU_2514/USA300HOU_2515 | HAD superfamily hydrolase/ABC superfamily ATP binding cassette transporter, ABC protein |
| ? | CP000730 | 2661832 = | 90 (1.070) | intergenic (‑225/‑96) | USA300HOU_2514/USA300HOU_2515 | HAD superfamily hydrolase/ABC superfamily ATP binding cassette transporter, ABC protein | |||||
| * | ? | CP000730 | = 614109 | 142 (1.490) | 9 (0.090) | 4/286 | 10.9 | 7.2% | coding (2421/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | 618412 = | 91 (0.960) | coding (3514/4146 nt) | sdrD | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD | |||||
| * | ? | CP000730 | 52495 = | 75 (0.790) | 134 (1.420) +T |
4/284 | 10.9 | 61.9% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 91 (0.960) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||