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 56 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 76,295 | 0 | T | C | 63.9% | 258.3 / 310.7 | 368 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 76,322 | 0 | G | A | 61.6% | 162.4 / inf | 354 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 36,087 | 0 | A | G | 60.1% | 293.6 / inf | 440 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,861 | 0 | T | C | 59.7% | 43.4 / 67.4 | 72 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 58.9% | 45.6 / 71.4 | 73 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 58.1% | 16.7 / 96.8 | 74 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 76,353 | 0 | G | A | 57.5% | 71.2 / 313.8 | 277 | intergenic (+411/‑723) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,867 | 0 | G | T | 57.3% | 11.9 / 103.4 | 75 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,315 | 0 | G | A | 56.8% | 156.6 / inf | 594 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 56.7% | 145.6 / 287.8 | 269 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,842 | 0 | T | . | 56.6% | 24.1 / 147.2 | 76 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 56.6% | 24.9 / 146.6 | 76 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 56.6% | 50.4 / 90.0 | 76 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 56.6% | 20.3 / 85.1 | 76 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,124 | 0 | G | A | 56.2% | 71.3 / inf | 337 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,866 | 0 | G | T | 56.2% | 3.3 / 106.3 | 75 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 55.8% | 1.2 / 106.3 | 78 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,269 | 0 | C | T | 55.3% | 52.2 / inf | 585 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 512,643 | 0 | A | G | 54.3% | 28.8 / 119.9 | 105 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 1,929,862 | 1 | . | T | 52.1% | 126.8 / 135.9 | 72 | intergenic (‑945/‑223) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 1205323 | 45 (0.960) | 29 (0.870) +38 bp |
8/190 | 3.4 | 47.4% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 2478252 = | 45 (0.960) | intergenic (+139/+932) | USA300HOU_2340/htrB | hypothetical membrane protein/hemin ABC superfamily ATP binding cassette transporter, ABC protein | |||||
| * | ? | CP000730 | = 1205323 | 45 (0.960) | 29 (0.870) +38 bp |
8/190 | 3.4 | 48.9% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | = 2072043 | 40 (0.860) | intergenic (+538/+35) | ykgB/USA300HOU_1927 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | = 1205323 | 45 (0.960) | 29 (0.870) +38 bp |
8/190 | 3.4 | 47.4% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | = 1443739 | NA (NA) | intergenic (‑312/+41) | USA300HOU_1341/brnQ2 | IS1272 transposase/LIVCS family branched chain amino acid:cation symporter | |||||
| * | ? | CP000730 | = 1205323 | 45 (0.960) | 29 (0.870) +38 bp |
8/190 | 3.4 | 45.3% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 1426517 = | 53 (1.140) | intergenic (‑248/+724) | pstS/yitL | phosphate ABC superfamily ATP binding cassette transporter, binding protein/hypothetical protein | |||||
| * | ? | CP000730 | = 2088038 | 42 (0.900) | 8 (0.200) | 8/232 | 4.3 | 18.1% | intergenic (+55/+1025) | chp/sak | chemotaxis inhibitory protein CHIPS/staphylokinase |
| ? | CP000730 | = 2088052 | 36 (0.880) | intergenic (+69/+1011) | chp/sak | chemotaxis inhibitory protein CHIPS/staphylokinase | |||||
| * | ? | CP000730 | = 1454029 | 48 (1.030) | 9 (0.210) | 8/242 | 4.5 | 16.9% | intergenic (‑108/+176) | sucA/arlS | oxoglutarate dehydrogenase (succinyl‑transferring) E1/sensor histidine kinase |
| ? | CP000730 | = 1454035 | 45 (1.060) | intergenic (‑114/+170) | sucA/arlS | oxoglutarate dehydrogenase (succinyl‑transferring) E1/sensor histidine kinase | |||||
| * | ? | CP000730 | 1097237 = | 43 (0.920) | 8 (0.190) | 8/246 | 4.6 | 15.6% | intergenic (+11/‑122) | cydB/ktrC | cytochrome d ubiquinol oxidase subunit II/possible Trk family potassium (K+) transporter, NAD+ binding protein |
| ? | CP000730 | 1097291 = | 47 (1.090) | intergenic (+65/‑68) | cydB/ktrC | cytochrome d ubiquinol oxidase subunit II/possible Trk family potassium (K+) transporter, NAD+ binding protein | |||||
| * | ? | CP000730 | 365029 = | 54 (1.160) | 8 (0.190) | 6/242 | 5.4 | 14.4% | intergenic (+39/+66) | nupC/USA300HOU_0334 | possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter |
| ? | CP000730 | 365083 = | 46 (1.080) | intergenic (+93/+12) | nupC/USA300HOU_0334 | possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter | |||||
| * | ? | CP000730 | = 9682 | 35 (0.800) | 12 (0.270) +AGATGA |
5/236 | 5.7 | 23.6% | coding (2651/2664 nt) | gyrA | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| ? | CP000730 | 9683 = | 44 (0.940) | coding (2652/2664 nt) | gyrA | DNA topoisomerase (ATP‑hydrolyzing) subunit A | |||||
| * | ? | CP000730 | 704277 = | 52 (1.110) | 6 (0.130) | 6/264 | 5.8 | 10.4% | intergenic (+27/+1133) | nhaK/psaA | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1/ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | 2290693 = | NA (NA) | intergenic (‑107/‑119) | arg/USA300HOU_2155 | arginase/transposase | |||||