| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,129,388 | C→T | 8.5% | intergenic (+221/+17) | 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 | 2,129,388 | 0 | C | T | 8.5% | 958.7 / 47.8 | 300 | intergenic (+221/+17) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Reads supporting (aligned to +/- strand): ref base C (142/132); new base T (10/16); total (152/148) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.22e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 305 total aligned reads displayed.
TCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCATATAATG > USA300TCH1516_ALE/2129298‑2129478 | ctACACGCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCa > 1:3069809/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAg > 2:2425507/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCCATGTAGCAg > 2:825787/1‑91 (MQ=255) acacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTAAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAgg > 2:3474772/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367377/1‑91 (MQ=255) gcTCAAACAAGATTCATACACTGCACGGCATAATTATTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCa < 2:3906949/90‑1 (MQ=255) acTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCa < 1:305667/91‑1 (MQ=255) tCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAAc > 1:960839/1‑91 (MQ=255) cAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACt < 1:2612818/91‑1 (MQ=255) aaaCAAGATTCATACACTGCACGTTATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtt < 2:3681269/91‑1 (MQ=255) aaaCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtt < 2:1201540/91‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt > 2:3843796/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 2:3031289/91‑1 (MQ=17) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:1946037/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:666673/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta < 1:494761/91‑1 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat < 2:2894680/91‑1 (MQ=255) aGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatt > 1:808905/1‑91 (MQ=255) gATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatta > 1:488175/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:105076/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:145970/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 1:2075609/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 2:3132342/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc < 1:2386287/91‑1 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt > 1:2804467/1‑91 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt < 2:2375416/91‑1 (MQ=255) tCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAGCTTTTATTACtt < 1:3024570/91‑1 (MQ=255) gcATACGCTGCACGTCGTAATATATCTATCTATTGAAATAGAATTAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTGCtt < 2:1708713/90‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:2080267/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:223364/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 1:368359/91‑1 (MQ=255) aTACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAt < 1:1764193/91‑1 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt > 1:334415/1‑91 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3577849/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 1:1390055/1‑91 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt < 1:93958/91‑1 (MQ=255) gCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtttt < 1:2599632/91‑1 (MQ=255) gCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtttt < 1:3626772/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:900542/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc > 2:3529288/1‑91 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 1:293183/91‑1 (MQ=255) aCGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtca > 1:2133136/1‑91 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 2:3291066/91‑1 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcctt > 2:3303472/1‑91 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 1:721085/1‑91 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 2:18470/91‑1 (MQ=255) aataaACCTATCTATTCAAATATACATAAAAGTTACCTACTACAATCTATGTACCAGGCAACTTTTATTACTTATTTCTTTtcattatcat > 2:2559474/1‑91 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt < 1:3860062/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa > 1:1879843/1‑91 (MQ=255) aaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAg > 1:3087101/1‑91 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:1677655/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3409610/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 1:3480396/91‑1 (MQ=255) tctatctaTTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTa < 2:2351591/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTAc < 1:3393414/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACGACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTAc < 1:3917874/91‑1 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtt > 1:1918300/1‑91 (MQ=255) tctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACttt > 2:547590/1‑91 (MQ=255) ttCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACa < 2:1602298/91‑1 (MQ=255) tCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACaa < 1:5530/91‑1 (MQ=255) aaTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACt > 1:979569/1‑91 (MQ=255) tataAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTc < 1:881884/91‑1 (MQ=255) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:3795675/4‑91 (MQ=14) gtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac > 2:127367/3‑91 (MQ=17) aaataaaAGTTACCTCCTACATTCTATGTAGCAGGCAACTTTTATTACTTATTGCTTATCATTATCATGAAGTGCTTTTATAAACTTcacc > 2:3541576/1‑90 (MQ=255) aaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcaca > 2:636250/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:2995042/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3608818/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3694442/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:1383188/1‑91 (MQ=255) ataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAtt > 2:1294717/1‑91 (MQ=17) taaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTa < 1:2874560/91‑1 (MQ=255) taaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTa > 1:2042542/1‑91 (MQ=255) aaaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAt > 2:3492788/1‑91 (MQ=255) aaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtg > 1:1813722/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 2:1767609/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 1:1649240/1‑91 (MQ=255) aGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgtg > 1:2473740/1‑91 (MQ=255) ttACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTc > 2:2763453/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt < 2:151119/91‑1 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:3212737/1‑91 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt < 2:1407829/91‑1 (MQ=255) ccTACTCCATTCTATGTAGCAGGCAACTTTTATCACTTATTTCTTTTCTTTTTCATTCAGTCCTTTTACCAACTTCACATCACGTGACTTc > 2:1102586/1‑91 (MQ=255) ccTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTc > 2:362955/1‑91 (MQ=255) ctactaCATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTcc < 1:1305177/91‑1 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa > 2:2446039/1‑91 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa < 2:2064360/91‑1 (MQ=255) aTTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCACTCAAc > 2:2819935/1‑91 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt < 1:1593470/91‑1 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt < 1:3542244/91‑1 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc > 1:3184612/1‑91 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc > 1:1010619/1‑91 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc < 1:1506220/91‑1 (MQ=255) tATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCa > 2:455773/1‑91 (MQ=255) tATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCa > 1:3775748/1‑91 (MQ=255) aTGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCat < 2:1136642/91‑1 (MQ=255) aTGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCat > 1:1802150/1‑91 (MQ=255) tAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCAtata > 1:2219627/1‑91 (MQ=255) aGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCATATaa > 2:682565/1‑91 (MQ=255) gCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCATATAAt < 2:2723386/91‑1 (MQ=255) | TCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCATATAATG > USA300TCH1516_ALE/2129298‑2129478 |
| 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: ‑ |