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 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,861 | 0 | T | C | 70.7% | 578.0 / 221.7 | 353 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 69.0% | 571.9 / inf | 363 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 68.8% | 442.6 / 299.8 | 361 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 68.7% | 405.0 / 307.3 | 361 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 68.4% | 606.0 / 253.7 | 367 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 68.2% | 550.9 / inf | 364 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,875 | 0 | T | C | 68.1% | 521.9 / 279.0 | 368 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 67.9% | 428.2 / 308.4 | 368 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 67.6% | 431.3 / inf | 369 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,918 | 0 | A | G | 67.4% | 474.8 / 293.4 | 376 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,917 | 0 | C | T | 66.8% | 416.1 / inf | 376 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,866 | 0 | G | T | 66.5% | 350.5 / 304.9 | 361 | intergenic (‑949/‑219) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,928 | 0 | T | A | 64.0% | 312.6 / inf | 322 | intergenic (‑1011/‑157) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,925 | 0 | T | A | 63.5% | 309.2 / inf | 322 | intergenic (‑1008/‑160) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,930 | 0 | T | A | 63.5% | 311.0 / inf | 322 | intergenic (‑1013/‑155) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,087 | 0 | A | G | 63.1% | 1840.4 / inf | 2105 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 62.2% | 1288.6 / inf | 1579 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,124 | 0 | G | A | 61.9% | 991.2 / inf | 1572 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 36,269 | 0 | C | T | 61.2% | 781.7 / inf | 2009 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 76,322 | 0 | G | A | 60.7% | 622.3 / inf | 1286 | intergenic (+380/‑754) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| Marginal new junction evidence (lowest skew 10 of 34 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 1205323 | 104 (0.790) | 26 (0.270) +38 bp |
8/218 | 6.1 | 22.1% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 2478252 = | 143 (1.090) | intergenic (+139/+932) | USA300HOU_2340/htrB | hypothetical membrane protein/hemin ABC superfamily ATP binding cassette transporter, ABC protein | |||||
| * | ? | CP000730 | = 1205323 | 104 (0.790) | 26 (0.270) +38 bp |
8/218 | 6.1 | 26.0% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | = 2072043 | 96 (0.730) | intergenic (+538/+35) | ykgB/USA300HOU_1927 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | = 1205323 | 104 (0.790) | 26 (0.270) +38 bp |
8/218 | 6.1 | 25.3% | 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 | 104 (0.790) | 26 (0.270) +38 bp |
8/218 | 6.1 | 27.4% | intergenic (+459/‑365) | yfiE/lspA | possible lactoylglutathione lyase/A8 family signal peptidase II |
| ? | CP000730 | 1426517 = | 82 (0.620) | intergenic (‑248/+724) | pstS/yitL | phosphate ABC superfamily ATP binding cassette transporter, binding protein/hypothetical protein | |||||
| * | ? | CP000730 | = 2001402 | NA (NA) | 10 (0.080) +CTCCTACAGG |
7/274 | 7.7 | 60.5% | intergenic (‑11/+205) | rrl3/USA300HOU_t0051 | 23S ribosomal RNA/tRNA‑Ala |
| ? | CP000730 | 2001459 = | 7 (0.050) | intergenic (‑68/+148) | rrl3/USA300HOU_t0051 | 23S ribosomal RNA/tRNA‑Ala | |||||
| * | ? | CP000730 | = 514638 | 9 (0.070) | 10 (0.080) +CCTGTAGGAG |
7/274 | 7.7 | 54.4% | intergenic (+306/‑68) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | CP000730 | 514695 = | NA (NA) | intergenic (+363/‑11) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | CP000730 | = 516939 | NA (NA) | 8 (0.060) | 7/282 | 7.9 | NA | noncoding (2234/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | = 516944 | NA (NA) | noncoding (2239/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | 633406 = | 117 (0.890) | 6 (0.050) | 6/282 | 8.3 | 4.7% | intergenic (+130/‑414) | proP/vraA | MFS family major facilitator transporter, proline/betaine:cation symporter/long‑chain‑fatty‑acid‑‑CoA ligase |
| ? | CP000730 | 633436 = | 129 (1.020) | intergenic (+160/‑384) | proP/vraA | MFS family major facilitator transporter, proline/betaine:cation symporter/long‑chain‑fatty‑acid‑‑CoA ligase | |||||
| * | ? | CP000730 | 1454018 = | 96 (0.730) | 8 (0.070) | 5/270 | 8.6 | 8.1% | intergenic (‑97/+187) | sucA/arlS | oxoglutarate dehydrogenase (succinyl‑transferring) E1/sensor histidine kinase |
| ? | CP000730 | 1454048 = | 94 (0.780) | intergenic (‑127/+157) | sucA/arlS | oxoglutarate dehydrogenase (succinyl‑transferring) E1/sensor histidine kinase | |||||
| * | ? | CP000730 | 2440041 = | 105 (0.800) | 4 (0.030) | 4/270 | 9.1 | 3.8% | intergenic (+2/+64) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC |
| ? | CP000730 | 2440099 = | 107 (0.890) | intergenic (+60/+6) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC | |||||