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 74 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,843 | 0 | A | . | 62.9% | 62.8 / 113.9 | 70 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 62.0% | 61.2 / 118.0 | 71 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 61.1% | 32.7 / 91.8 | 72 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,970 | 0 | T | C | 59.9% | 202.7 / 246.3 | 253 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,087 | 0 | A | G | 59.8% | 258.0 / inf | 393 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,861 | 0 | T | C | 59.5% | 48.2 / 69.7 | 74 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,269 | 0 | C | T | 58.2% | 115.3 / inf | 421 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,867 | 0 | G | T | 57.1% | 15.8 / 103.9 | 77 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,124 | 0 | G | A | 56.8% | 70.0 / inf | 288 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 76,295 | 0 | T | C | 56.8% | 118.7 / 312.6 | 304 | intergenic (+353/‑781) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 76,322 | 0 | G | A | 56.7% | 66.7 / inf | 284 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 1,929,870 | 0 | A | C | 56.4% | 51.8 / 96.4 | 78 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 56.4% | 15.3 / 91.4 | 78 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,315 | 0 | G | A | 56.2% | 115.2 / inf | 485 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,866 | 0 | G | T | 56.0% | 1.5 / 110.9 | 77 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 512,643 | 0 | A | G | 55.7% | 17.0 / 75.5 | 70 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 1,929,873 | 0 | C | A | 55.7% | 1.4 / 115.3 | 79 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 55.7% | 34.9 / 85.6 | 79 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,413 | 0 | C | T | 55.0% | 36.0 / 314.1 | 271 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,812 | 0 | G | A | 52.7% | ‑5.9 / 70.1 | 55 | intergenic (‑895/‑273) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 2431654 | 42 (1.220) | 7 (0.230) +CTATGGAGTCGATGGGGT |
5/230 | 3.8 | 18.4% | intergenic (+1/+646) | USA300HOU_2294/USA300HOU_2296 | transcriptional regulator/hypothetical membrane protein |
| ? | CP000730 | 2432295 = | 30 (0.870) | intergenic (+642/+5) | USA300HOU_2294/USA300HOU_2296 | transcriptional regulator/hypothetical membrane protein | |||||
| * | ? | CP000730 | = 1856676 | 26 (0.750) | 5 (0.150) | 5/254 | 4.1 | 16.7% | intergenic (‑361/+339) | aroA/USA300HOU_1728 | bifunctional chorismate mutase/3‑deoxy‑7‑phosphoheptulonate synthase/hypothetical protein |
| ? | CP000730 | 1856683 = | 25 (0.760) | intergenic (‑368/+332) | aroA/USA300HOU_1728 | bifunctional chorismate mutase/3‑deoxy‑7‑phosphoheptulonate synthase/hypothetical protein | |||||
| * | ? | CP000730 | = 208036 | 27 (0.780) | 5 (0.150) | 5/252 | 4.1 | 15.2% | coding (4445/7194 nt) | USA300HOU_0192 | non‑ribosomal peptide synthetase |
| ? | CP000730 | = 208062 | 30 (0.920) | coding (4471/7194 nt) | USA300HOU_0192 | non‑ribosomal peptide synthetase | |||||
| * | ? | CP000730 | = 536990 | 37 (1.070) | 5 (0.150) | 5/262 | 4.3 | 12.0% | intergenic (+183/‑128) | rplY/pth | ribosomal protein L25/aminoacyl‑tRNA hydrolase |
| ? | CP000730 | = 1995778 | 37 (1.090) | intergenic (+31/+62) | USA300HOU_1855/USA300HOU_t0025 | IS1181 transposase/tRNA‑Leu | |||||
| * | ? | CP000730 | = 613916 | 38 (1.100) | 4 (0.120) | 4/256 | 4.6 | 9.7% | coding (2228/2844 nt) | sdrC | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| ? | CP000730 | 618273 = | 38 (1.150) | coding (3375/4146 nt) | sdrD | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD | |||||
| * | ? | CP000730 | 2716786 = | 40 (1.160) | 4 (0.120) | 4/264 | 4.8 | 10.0% | intergenic (+94/+56) | ynzC/USA300HOU_2569 | hypothetical protein/possible lactoylglutatione lyase |
| ? | CP000730 | 2866775 = | 32 (0.940) | intergenic (‑174/+279) | USA300HOU_2711/noc | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 1217678 = | 28 (0.810) | 3 (0.100) | 3/234 | 4.8 | 9.9% | intergenic (+7/‑430) | USA300HOU_1144/USA300HOU_1145 | hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase |
| ? | CP000730 | 1217746 = | 30 (0.990) | intergenic (+75/‑362) | USA300HOU_1144/USA300HOU_1145 | hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase | |||||
| * | ? | CP000730 | 1287796 = | 16 (0.460) | 3 (0.090) | 3/246 | 5.0 | 12.0% | intergenic (+44/‑246) | dnaE1/rimP | DNA‑directed DNA polymerase III alpha subunit/hypothetical protein |
| ? | CP000730 | 1287846 = | 29 (0.910) | intergenic (+94/‑196) | dnaE1/rimP | DNA‑directed DNA polymerase III alpha subunit/hypothetical protein | |||||
| * | ? | CP000730 | = 1144514 | 28 (0.810) | 3 (0.090) | 3/248 | 5.0 | 9.8% | coding (29/108 nt) | USA300HOU_1070 | hypothetical protein |
| ? | CP000730 | = 1144528 | 29 (0.900) | coding (43/108 nt) | USA300HOU_1070 | hypothetical protein | |||||
| * | ? | CP000730 | 37094 = | 38 (1.100) | 3 (0.090) | 3/246 | 5.0 | 7.9% | coding (21/231 nt) | USA300HOU_0028 | hypothetical protein |
| ? | CP000730 | 37188 = | 35 (1.100) | coding (115/231 nt) | USA300HOU_0028 | hypothetical protein | |||||