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 | 35,876 | 0 | C | T | 63.2% | 3.8 / inf | 466 | intergenic (+107/+1) | rlmH/tpn | hypothetical protein/IS431mec transposase |
| * | CP000730 | 35,970 | 0 | T | C | 63.0% | 1261.0 / inf | 1482 | E194E (GAA→GAG) | tpn | IS431mec transposase |
| * | CP000730 | 36,087 | 0 | A | G | 62.3% | 1852.4 / inf | 2164 | C155C (TGT→TGC) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,918 | 0 | A | G | 60.9% | 286.9 / inf | 340 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,861 | 0 | T | C | 60.5% | 303.4 / 315.9 | 338 | intergenic (‑944/‑224) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,867 | 0 | G | T | 60.5% | 200.8 / inf | 339 | intergenic (‑950/‑218) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,873 | 0 | C | A | 60.5% | 177.2 / inf | 345 | intergenic (‑956/‑212) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,917 | 0 | C | T | 60.5% | 200.0 / inf | 340 | intergenic (‑1000/‑168) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,124 | 0 | G | A | 60.2% | 919.5 / inf | 1624 | A143V (GCT→GTT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,875 | 0 | T | C | 59.2% | 276.5 / inf | 345 | intergenic (‑958/‑210) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,842 | 0 | T | . | 59.2% | 181.2 / inf | 341 | intergenic (‑925/‑243) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,843 | 0 | A | . | 59.2% | 165.6 / inf | 347 | intergenic (‑926/‑242) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,872 | 0 | G | A | 59.0% | 165.9 / inf | 348 | intergenic (‑955/‑213) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,870 | 0 | A | C | 58.8% | 351.0 / inf | 347 | intergenic (‑953/‑215) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,848 | 0 | C | A | 58.5% | 140.5 / inf | 347 | intergenic (‑931/‑237) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,269 | 0 | C | T | 58.1% | 467.3 / inf | 2059 | A95T (GCA→ACA) | tpn | IS431mec transposase |
| * | CP000730 | 36,315 | 0 | G | A | 58.0% | 565.4 / inf | 2092 | Y79Y (TAC→TAT) | tpn | IS431mec transposase |
| * | CP000730 | 1,929,930 | 0 | T | A | 57.8% | 130.0 / inf | 285 | intergenic (‑1013/‑155) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 1,929,928 | 0 | T | A | 57.6% | 106.0 / inf | 285 | intergenic (‑1011/‑157) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| * | CP000730 | 36,413 | 0 | C | T | 57.4% | 223.1 / inf | 1223 | V47I (GTC→ATC) | tpn | IS431mec transposase |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 848580 | 138 (1.090) | 8 (0.070) +CTGAAAAAAAAAA |
7/270 | 5.5 | 5.4% | coding (101/312 nt) | USA300HOU_0793 | hypothetical protein |
| ? | CP000730 | 2866847 = | 167 (1.320) | intergenic (‑246/+207) | USA300HOU_2711/noc | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | = 848580 | 138 (1.090) | 7 (0.060) +CTGAAAAAAAAAAA |
5/268 | 6.2 | 5.1% | coding (101/312 nt) | USA300HOU_0793 | hypothetical protein |
| ? | CP000730 | 2665075 = | 151 (1.190) | intergenic (+310/‑168) | pat/USA300HOU_2519 | acetyltransferase/hypothetical protein | |||||
| * | ? | CP000730 | 512969 = | NA (NA) | 11 (0.090) | 5/278 | 6.3 | NA | noncoding (177/1540 nt) | rrs1 | 16S ribosomal RNA |
| ? | CP000730 | 512991 = | NA (NA) | noncoding (199/1540 nt) | rrs1 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | 52495 = | 158 (1.250) | 186 (1.480) +T |
5/294 | 6.5 | 57.5% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 119 (0.940) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 801002 = | 117 (0.930) | 8 (0.070) +TTTTTTTTTTCAG |
4/270 | 6.7 | 6.4% | intergenic (+136/‑215) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | = 848580 | 138 (1.090) | coding (101/312 nt) | USA300HOU_0793 | hypothetical protein | |||||
| * | ? | CP000730 | = 800928 | 106 (0.840) | 4 (0.030) | 4/282 | 6.8 | 4.1% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 85 (0.710) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | 76096 = | 174 (1.380) | 8 (0.070) | 4/278 | 6.8 | 4.6% | intergenic (+154/‑980) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase |
| ? | CP000730 | 76124 = | 168 (1.410) | intergenic (+182/‑952) | USA300HOU_0072/USA300HOU_0075 | universal stress protein/lysophospholipase | |||||
| * | ? | CP000730 | 36133 = | 1690 (13.360) | 8 (0.070) | 4/284 | 6.9 | 0.49% | coding (419/675 nt) | tpn | IS431mec transposase |
| ? | CP000730 | 36148 = | 1642 (13.530) | coding (404/675 nt) | tpn | IS431mec transposase | |||||
| * | ? | CP000730 | 1708636 = | 121 (0.960) | 6 (0.050) | 3/268 | 7.1 | 5.1% | intergenic (+81/+121) | USA300HOU_1602/sem | hypothetical membrane protein/enterotoxin |
| ? | CP000730 | 1708685 = | 116 (1.010) | intergenic (+130/+72) | USA300HOU_1602/sem | hypothetical membrane protein/enterotoxin | |||||
| * | ? | CP000730 | = 1114106 | 87 (0.690) | 6 (0.050) | 3/262 | 7.1 | 7.1% | intergenic (+35/‑4) | USA300HOU_1045/USA300HOU_1046 | hypothetical membrane protein/hypothetical protein |
| ? | CP000730 | = 1114131 | 80 (0.720) | coding (22/105 nt) | USA300HOU_1046 | hypothetical protein | |||||