| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,129,372 | A→G | 7.5% | intergenic (+205/+33) | hlb_2 → / ← USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,129,372 | 0 | A | G | 7.5% | 868.1 / 38.3 | 278 | intergenic (+205/+33) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Reads supporting (aligned to +/- strand): ref base A (133/123); new base G (5/16); total (139/139) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.12e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 | |||||||||||
Only 100 of 292 total aligned reads displayed.
TAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAA > USA300TCH1516_ALE/2129282‑2129462 | tAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACcta > 1:280072/1‑91 (MQ=255)tAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACcta < 2:583442/91‑1 (MQ=255) tACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACctacta < 2:728435/91‑1 (MQ=255) tACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACctacta < 2:1897101/91‑1 (MQ=255) cAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACa < 2:1588424/91‑1 (MQ=255) cAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACa > 1:741514/1‑91 (MQ=255) aGTCTTGACTCTACACGCATACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACAtt < 2:650529/91‑1 (MQ=255) gTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTc < 1:2877399/91‑1 (MQ=255) gTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTc < 2:2047600/91‑1 (MQ=255) tCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACAtaga < 1:871690/91‑4 (MQ=39) cTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTa < 2:3390569/91‑1 (MQ=255) ctctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAg > 1:693618/1‑91 (MQ=255) tctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGc > 2:128948/1‑91 (MQ=255) ctACACGCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCa > 1:3069809/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAg > 2:2425507/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCCATGTAGCAg > 2:825787/1‑91 (MQ=255) acacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAgg > 2:1621074/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAACTAAAAGTTACCTACTACATTCTATGTAGCAGGc > 1:3508053/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367217/1‑91 (MQ=255) gcTCAAACAAGATTCATACACTGCACGGCATAATTATTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCa < 2:3906949/90‑1 (MQ=255) tCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAAc > 1:960839/1‑91 (MQ=255) cAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACt < 1:2612818/91‑1 (MQ=255) aaaCAAGATTCATACACTGCACGTAATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtt < 2:3681284/91‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt > 2:3843796/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:666673/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 2:3194058/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta > 2:1254570/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta > 1:2181313/1‑91 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttat < 2:2749402/91‑1 (MQ=18) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat < 2:2894680/91‑1 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat > 2:2809317/1‑91 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat < 2:3706309/91‑1 (MQ=255) aGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatt > 1:808905/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:105076/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 2:3131723/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 1:2075530/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc < 1:2386287/91‑1 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt < 1:450610/91‑1 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt < 2:2375416/91‑1 (MQ=255) tCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAGCTTTTATTACtt < 1:3024570/91‑1 (MQ=255) gcATACGCTGCACGTCGTAATATATCTATCTATTGAAATAGAATTAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTGCtt < 2:1708713/90‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAGTTa > 1:3064559/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:2080213/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa > 1:2845216/1‑91 (MQ=255) tACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAtt > 1:1930105/1‑91 (MQ=255) acacTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAttt < 2:1112715/91‑1 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3577827/91‑1 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt > 1:334415/1‑91 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 2:3497249/1‑91 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt < 1:93958/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 1:1401461/1‑91 (MQ=255) gCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtttt < 1:2599632/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:3595697/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:900542/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 1:1712957/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 1:293183/91‑1 (MQ=255) cGTCATAATAAATATATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:548778/91‑1 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 2:2227526/1‑91 (MQ=255) cATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattat > 1:1889198/1‑91 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 2:18315/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca < 2:1394273/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca > 1:1466094/1‑91 (MQ=255) aataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcat > 1:3872239/1‑91 (MQ=255) aataaACCTATCTATTCAAATATACATAAAAGTTACCTACTACAATCTATGTACCAGGCAACTTTTATTACTTATTTCTTTtcattatcat > 2:2559474/1‑91 (MQ=255) taaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatta < 1:1362140/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa < 1:489179/91‑1 (MQ=255) aaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAg < 2:3614580/91‑1 (MQ=255) aaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAg > 1:3087101/1‑91 (MQ=255) atctatctATTCTAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACCTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3292364/91‑1 (MQ=255) atctatctATTCAAATATAAATAAGAGTTACCTACTACATTCTATGTAGCGGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3675068/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:1677655/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 1:3480396/91‑1 (MQ=255) tctatctaTTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTa < 2:2351591/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTAc < 1:3393414/91‑1 (MQ=255) tatctatTCAAATATAAATAAAAGTGACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACt < 1:3676943/91‑1 (MQ=255) tctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACttt > 2:547590/1‑91 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3613534/91‑1 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3703108/91‑1 (MQ=255) ctatTCAAATATAAAAGAACGTTACCTACTACGTGCTATGTAGCAGGCCACTTTTATTACTTATTTCTTTTCATTATCAGTAAGTACtttt < 2:1100531/91‑1 (MQ=255) atTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTAc < 2:3472694/91‑1 (MQ=255) atTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTAc < 2:3486883/91‑1 (MQ=255) cAAATATAAATAAAAGTTACCTACTACATTCCCTGTAGCAGGCAACTTTTATTACTTATTTCTTTTCGCTATCATTAAGCACTTTTACaaa > 2:3022224/1‑91 (MQ=255) aaTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACt > 1:979569/1‑91 (MQ=255) atatAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACtt > 1:1790012/1‑91 (MQ=255) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:3795675/4‑91 (MQ=14) taaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac < 1:1618282/91‑1 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCCCAt > 1:1032296/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3539717/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt < 1:2127058/91‑1 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:2995042/1‑91 (MQ=255) taaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTa > 1:2042542/1‑91 (MQ=255) aaaGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTACCATTAAGTACTTTTACAAACTTCCCATTAtg > 2:1343929/1‑91 (MQ=18) aaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtg > 1:1813722/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 2:1767609/1‑91 (MQ=255) aGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgtg > 1:2473740/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt < 2:151119/91‑1 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:3212737/1‑91 (MQ=255) ctactaCATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTcc < 1:1305177/91‑1 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa > 2:2446039/1‑91 (MQ=255) actacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCaa < 1:3828556/91‑1 (MQ=255) | TAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAA > USA300TCH1516_ALE/2129282‑2129462 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |