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 50 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 36,315 | 0 | G | A | 58.9% | 381.9 / inf | 803 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 58.2% | 226.2 / inf | 406 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,413 | 0 | C | T | 58.1% | 160.1 / inf | 435 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| * | CP000730 | 36,269 | 0 | C | T | 56.6% | 104.8 / inf | 746 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 76,295 | 0 | T | C | 54.6% | 156.2 / inf | 597 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 36,087 | 0 | A | G | 53.9% | 195.1 / inf | 635 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 76,322 | 0 | G | A | 52.8% | 66.1 / inf | 552 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 35,876 | 0 | C | T | 52.5% | 58.3 / 139.4 | 99 | intergenic (+107/+1) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 36,124 | 0 | G | A | 51.4% | 22.9 / inf | 458 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 36,444 | 0 | C | T | 49.8% | 53.7 / inf | 287 | R36R (AGG→AGA) | tpn | IS431mec transposase |
| * | CP000730 | 76,353 | 0 | G | A | 49.8% | 24.5 / inf | 448 | intergenic (+411/‑723) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 512,643 | 0 | A | G | 45.1% | 36.4 / 201.2 | 154 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 35,858 | 0 | T | A | 43.1% | 109.6 / 105.2 | 72 | intergenic (+89/+19) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 1,929,843 | 0 | A | . | 42.2% | 230.9 / 189.5 | 109 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 41.8% | 233.6 / 189.6 | 110 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,861 | 0 | T | C | 41.5% | 48.2 / 130.8 | 106 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 40.4% | 49.5 / 131.3 | 109 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 40.4% | 122.5 / 135.8 | 114 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 40.2% | 23.8 / 169.8 | 112 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 39.6% | 78.4 / 125.4 | 111 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 2252589 = | 88 (1.250) | 9 (0.140) | 7/252 | 8.3 | 9.8% | intergenic (+25/+127) | luxS/USA300HOU_2124 | S‑ribosylhomocysteine lyase/hypothetical membrane protein |
| ? | CP000730 | 2252638 = | 84 (1.270) | intergenic (+74/+78) | luxS/USA300HOU_2124 | S‑ribosylhomocysteine lyase/hypothetical membrane protein | |||||
| * | ? | CP000730 | = 1040370 | 52 (0.740) | 5 (0.080) | 5/242 | 9.1 | 9.1% | intergenic (‑6787/‑919) | USA300HOU_0983/USA300HOU_0984 | competence protein/glycosyltransferase |
| ? | CP000730 | = 1040397 | 53 (0.840) | intergenic (‑6814/‑892) | USA300HOU_0983/USA300HOU_0984 | competence protein/glycosyltransferase | |||||
| * | ? | CP000730 | 431138 = | 63 (0.890) | 5 (0.080) | 5/250 | 9.3 | 7.6% | intergenic (+16/+65) | nfrA/tcyP | possible FMN reductase/possible DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| ? | CP000730 | 431188 = | 63 (0.960) | intergenic (+66/+15) | nfrA/tcyP | possible FMN reductase/possible DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter | |||||
| * | ? | CP000730 | 2256396 = | 79 (1.120) | 4 (0.060) | 4/242 | 9.8 | 5.6% | intergenic (+49/+72) | deoD2/dps | purine‑nucleoside phosphorylase/Dps family stress protein |
| ? | CP000730 | 2256443 = | 63 (0.990) | intergenic (+96/+25) | deoD2/dps | purine‑nucleoside phosphorylase/Dps family stress protein | |||||
| * | ? | CP000730 | 739788 = | 60 (0.850) | 6 (0.090) | 4/244 | 9.8 | 10.4% | intergenic (+15/+573) | pitA/sle1 | possible PiT family inorganic phosphate transporter/possible LysM domain protein |
| ? | CP000730 | 739837 = | 49 (0.770) | intergenic (+64/+524) | pitA/sle1 | possible PiT family inorganic phosphate transporter/possible LysM domain protein | |||||
| * | ? | CP000730 | 2476442 = | 67 (0.950) | 4 (0.060) | 4/246 | 9.9 | 6.2% | intergenic (‑187/+53) | tcaA/tcaR | teicoplanin resistance protein TcaA/transcriptional regulator TcaR |
| ? | CP000730 | 2476489 = | 61 (0.950) | intergenic (‑234/+6) | tcaA/tcaR | teicoplanin resistance protein TcaA/transcriptional regulator TcaR | |||||
| * | ? | CP000730 | = 1955657 | 64 (0.910) | 4 (0.060) | 4/248 | 9.9 | 6.5% | intergenic (‑502/+411) | USA300HOU_1816/lukD | hypothetical protein/leukotoxin LukD |
| ? | CP000730 | = 1955663 | 56 (0.860) | intergenic (‑508/+405) | USA300HOU_1816/lukD | hypothetical protein/leukotoxin LukD | |||||
| * | ? | CP000730 | 1873411 = | 100 (1.410) | 3 (0.050) | 3/244 | 10.5 | 3.5% | intergenic (‑87/+663) | USA300HOU_1742/USA300HOU_1743 | M20 family peptidase/hypothetical protein |
| ? | CP000730 | 1873475 = | 73 (1.140) | intergenic (‑151/+599) | USA300HOU_1742/USA300HOU_1743 | M20 family peptidase/hypothetical protein | |||||
| * | ? | CP000730 | = 1205323 | 69 (0.980) | 33 (0.470) | 4/270 | 10.5 | 30.7% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 1205383 = | 80 (1.130) | intergenic (+519/‑305) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II | |||||
| * | ? | CP000730 | 468257 = | 94 (1.330) | 3 (0.050) | 3/246 | 10.6 | 3.4% | coding (638/792 nt) | USA300HOU_0443 | hypothetical lipoprotein |
| ? | CP000730 | 468356 = | 86 (1.340) | coding (737/792 nt) | USA300HOU_0443 | hypothetical lipoprotein | |||||