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 57 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,918 | 0 | A | G | 72.2% | 1255.3 / inf | 783 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,917 | 0 | C | T | 72.0% | 1081.1 / inf | 783 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,861 | 0 | T | C | 71.9% | 1261.5 / inf | 763 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 71.8% | 1047.8 / inf | 766 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 71.8% | 1275.4 / inf | 763 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 71.6% | 1049.9 / inf | 767 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 71.5% | 1015.4 / inf | 766 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 71.4% | 1404.7 / inf | 769 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 70.2% | 969.1 / inf | 778 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 70.0% | 1313.2 / inf | 777 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 69.5% | 1286.5 / inf | 773 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,866 | 0 | G | T | 69.4% | 865.2 / inf | 767 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,925 | 0 | T | A | 68.7% | 855.3 / inf | 659 | intergenic (‑1008/‑160) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,928 | 0 | T | A | 68.5% | 843.5 / inf | 659 | intergenic (‑1011/‑157) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,930 | 0 | T | A | 68.4% | 848.2 / inf | 659 | intergenic (‑1013/‑155) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 35,876 | 0 | C | T | 67.1% | 345.0 / inf | 1000 | intergenic (+107/+1) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 64.5% | 3170.1 / inf | 3369 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 76,180 | 0 | C | T | 63.6% | 214.4 / inf | 568 | intergenic (+238/‑896) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| * | CP000730 | 36,269 | 0 | C | T | 63.5% | 2214.7 / inf | 4347 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,941 | 0 | A | T | 63.3% | 578.1 / inf | 592 | intergenic (‑1024/‑144) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 68659 = | 131 (0.690) | 11 (0.070) | 11/260 | 12.4 | 8.7% | coding (775/852 nt) | USA300HOU_0065 | transposase |
| ? | CP000730 | = 68655 | 115 (0.690) | coding (771/852 nt) | USA300HOU_0065 | transposase | |||||
| * | ? | CP000730 | 52495 = | 143 (0.760) | 226 (1.210) +T |
8/294 | 15.4 | 63.3% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 121 (0.640) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 52489 = | 150 (0.790) | 37 (0.220) | 6/266 | 15.6 | 23.0% | intergenic (+99/‑574) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52983 | 113 (0.670) | intergenic (+593/‑80) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 705321 = | 188 (1.000) | 5 (0.030) | 5/278 | 16.8 | 2.7% | intergenic (+1071/+89) | nhaK/psaA | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1/ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | 705378 = | 189 (1.070) | intergenic (+1128/+32) | nhaK/psaA | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1/ABC superfamily ATP binding cassette transporter, binding protein | |||||
| * | ? | CP000730 | = 800928 | 211 (1.120) | 6 (0.030) | 5/282 | 17.0 | 3.0% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 183 (1.020) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | = 514456 | 199 (1.050) | 250 (1.360) | 5/288 | 17.2 | 57.0% | intergenic (+124/‑250) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | CP000730 | 514473 = | 183 (1.000) | intergenic (+141/‑233) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | CP000730 | = 1205323 | 177 (0.940) | 40 (0.210) | 5/296 | 17.5 | 18.5% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 1205383 = | 176 (0.930) | intergenic (+519/‑305) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II | |||||
| * | ? | CP000730 | 721319 = | 231 (1.220) | 10 (0.060) | 4/278 | 17.6 | 4.8% | coding (405/834 nt) | yxkD | hypothetical protein |
| ? | CP000730 | 721392 = | 183 (1.030) | coding (478/834 nt) | yxkD | hypothetical protein | |||||
| * | ? | CP000730 | = 76265 | 2881 (15.270) | 5 (0.030) | 4/284 | 17.9 | 0.18% | intergenic (+323/‑811) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| ? | CP000730 | = 76268 | 2937 (16.230) | intergenic (+326/‑808) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||
| * | ? | CP000730 | 36492 = | 364 (1.930) | 5 (0.030) | 4/284 | 17.9 | 0.33% | coding (60/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | = 76259 | 2716 (15.010) | intergenic (+317/‑817) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||