| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,129,379 | T→A | 7.0% | intergenic (+212/+26) | 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 | 2,129,379 | 0 | T | A | 7.0% | 916.5 / 39.5 | 279 | intergenic (+212/+26) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Reads supporting (aligned to +/- strand): ref base T (131/126); new base A (5/15); total (137/142) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.50e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 287 total aligned reads displayed.
AGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTT > USA300TCH1516_ALE/2129289‑2129469 | aGTCTTTACTCTACACTCAAACAAGATTCATCCACTGCACGTCATAATAAATCTATCTATTCAAATACAAATAAAAGTTGCCTACTACAtt > 2:3016594/1‑91 (MQ=255) gTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTc < 1:2877399/91‑1 (MQ=255) gTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTc < 2:2047600/91‑1 (MQ=255) cTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTa < 1:3486700/91‑1 (MQ=255) ttACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATg > 1:3517360/1‑91 (MQ=255) ttACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATg > 1:863434/1‑91 (MQ=255) tctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGc > 2:128948/1‑91 (MQ=255) gctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGc < 2:664314/90‑1 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCCATGTAGCAg > 2:825787/1‑91 (MQ=255) acacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAgg > 2:1621074/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367328/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc < 2:3708042/91‑1 (MQ=255) tCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAAc > 1:960839/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 2:3031289/91‑1 (MQ=17) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta > 2:1254570/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta < 1:494761/91‑1 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat > 2:2809317/1‑91 (MQ=255) aGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatt > 2:116503/1‑91 (MQ=255) gATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattt < 1:180728/91‑2 (MQ=17) gATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatta > 1:488175/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:105076/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 1:2126433/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 2:3132342/1‑91 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt < 2:2375416/91‑1 (MQ=255) tCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACtt > 1:3370192/1‑91 (MQ=255) gcATACGCTGCACGTCGTAATATATCTATCTATTGAAATAGAATTAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTGCtt < 2:1708713/90‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTATTTa > 1:3064575/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa > 1:18920/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa > 1:2845216/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:2080213/91‑1 (MQ=255) aTACACTGGTCGTCATAATAAATCTATCTATTCAACTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTGTATTACTTAt < 2:2507239/91‑1 (MQ=255) aTACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAt < 2:2644929/91‑1 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3811687/91‑1 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3577827/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 1:1401461/1‑91 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt < 1:93958/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 2:3497249/1‑91 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:900542/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:3595697/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 1:293183/91‑1 (MQ=255) aCGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtca > 1:2286989/1‑91 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat > 1:2586797/1‑91 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:80596/91‑1 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 2:2227526/1‑91 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 1:721085/1‑91 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 2:18470/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca < 2:1394273/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca > 1:1466094/1‑91 (MQ=255) aataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTacattatcat > 1:3792180/1‑91 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt < 1:3860062/91‑1 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt > 2:2838577/1‑91 (MQ=255) taaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatta < 1:1362140/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa > 1:1879832/1‑91 (MQ=255) aaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAg < 2:3617626/91‑1 (MQ=255) atctatctATTCTAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACCTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3292519/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 1:2611178/91‑1 (MQ=255) tctatctaTTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTa < 2:2351591/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTAc < 2:3894346/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACGACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTAc < 1:3917874/91‑1 (MQ=255) tatctatTCAAATATAAATAAAAGTTACCTACTACATTTTCTGTAACCAGCAACAGTTATTAATTATCTTTTTTCATTATCATTAAGTACt > 2:3675373/1‑91 (MQ=255) tatctatTCAAATATAAATAAAAGTGACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACt < 1:3676943/91‑1 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACATTTATTACATAATTCTTTTCATTATCATTAAGTACtt > 1:1939100/1‑91 (MQ=255) tctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACttt > 2:547784/1‑91 (MQ=255) ctatTCACATAGAAATGAAAGTTACCTACTACAGTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 2:2433771/91‑1 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3613534/91‑1 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3703108/91‑1 (MQ=255) tatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa < 1:3085330/91‑1 (MQ=255) tatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa > 1:681460/1‑91 (MQ=255) tatTCAAATATAAATAAAAGTTACATACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa < 2:3685667/91‑1 (MQ=255) atTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTAc < 2:3486883/91‑1 (MQ=255) atTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTAc < 2:3472694/91‑1 (MQ=255) ttCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACa > 2:405925/1‑91 (MQ=255) tCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACaa < 1:5530/91‑1 (MQ=255) tCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACaa > 1:3294593/1‑91 (MQ=255) aaaTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAAc < 1:2073622/91‑1 (MQ=255) aaTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACt > 1:979569/1‑91 (MQ=255) ataaataaAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca < 2:242538/91‑1 (MQ=255) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:2664347/4‑91 (MQ=14) taaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac < 1:1729576/91‑1 (MQ=255) taaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac > 2:1681113/1‑91 (MQ=255) aaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcaca > 2:636250/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCCCAt > 1:1032296/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3539717/1‑91 (MQ=255) taaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTa < 1:2985310/91‑1 (MQ=255) aaaGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTACCATTAAGTACTTTTACAAACTTCCCATTAtg > 2:1343929/1‑91 (MQ=18) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt < 1:3448263/91‑1 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 1:1649240/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 2:1767609/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt < 2:151119/91‑1 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:3212661/1‑91 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:2412462/1‑91 (MQ=255) ccTACTCCATTCTATGTAGCAGGCAACTTTTATCACTTATTTCTTTTCTTTTTCATTCAGTCCTTTTACCAACTTCACATCACGTGACTTc > 2:1102586/1‑91 (MQ=255) ccTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTc < 2:3274362/91‑1 (MQ=255) ctactaCATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTcc < 1:1305177/91‑1 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa < 1:2161272/91‑1 (MQ=255) tacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATc < 2:3403589/91‑1 (MQ=255) acATTCTATGCAGCAGGCAACTTTTCTTACTTATTTCTTTTCATTCTCATTAAGTACTTCTACAAACTTCACCTTCTGCGTCTCCCACTCa > 2:2937734/1‑91 (MQ=255) aTTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGGCTTCCAATCAAc < 1:3048466/91‑1 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt > 2:1556518/1‑91 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt < 1:1593470/91‑1 (MQ=255) | AGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTT > USA300TCH1516_ALE/2129289‑2129469 |
| 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: ‑ |