| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,129,368 | A→G | 8.1% | intergenic (+201/+37) | 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 | 2,129,368 | 0 | A | G | 8.1% | 881.3 / 42.9 | 280 | intergenic (+201/+37) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Reads supporting (aligned to +/- strand): ref base A (126/131); new base G (7/16); total (133/147) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.26e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 289 total aligned reads displayed.
TCATTAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTT > USA300TCH1516_ALE/2129278‑2129458 | tCATTAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTa > 1:2199284/1‑91 (MQ=255) aTTAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTAcc < 1:3893292/91‑1 (MQ=255) aTTAATACAAGTCTTGACTCTACACTCAAACAAGATGCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTAcc < 2:668264/91‑1 (MQ=255) ttAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACct < 1:2351306/91‑1 (MQ=255) tAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACcta < 2:583442/91‑1 (MQ=255) aTACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACctact < 2:2757036/91‑1 (MQ=255) tACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACctacta < 2:1897101/91‑1 (MQ=255) cAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACa < 2:1588424/91‑1 (MQ=255) aaGTCTTTACTCTACACTCAAACAAGATTCATACGCTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACAt < 2:3485003/91‑1 (MQ=255) aGTCTTTACTCTACACTCAAACAAGATTCATCCACTGCACGTCATAATAAATCTATCTATTCAAATACAAATAAAAGTTGCCTACTACAtt > 2:3016973/1‑91 (MQ=255) aGTCTTGACTCTACACGCATACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACAtt < 2:650529/91‑1 (MQ=255) gTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTc < 2:2047600/91‑1 (MQ=255) tCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACAtaga < 1:2438222/91‑4 (MQ=255) cTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTa < 1:3486700/91‑1 (MQ=255) ttACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATg > 1:863434/1‑91 (MQ=255) ttACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATg > 1:3517360/1‑91 (MQ=255) ctctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAg > 1:693618/1‑91 (MQ=255) tctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGc > 2:128948/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAg > 2:2425520/1‑91 (MQ=255) acacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAgg > 2:1621074/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367217/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367377/1‑91 (MQ=255) gcTCAAACAAGATTCATACACTGCACGGCATAATTATTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCa < 2:3906949/90‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt > 2:2561163/1‑91 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt < 2:2818716/91‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt > 2:3843796/1‑91 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTACGTAGCAGGCAACtttt > 2:3035536/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:1946037/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:959250/91‑1 (MQ=17) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 2:3193874/91‑1 (MQ=17) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:666673/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTtta < 1:494761/91‑1 (MQ=255) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttat < 2:3706309/91‑1 (MQ=255) aGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatt > 2:116503/1‑91 (MQ=255) gATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTttatta > 1:488175/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:105076/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 1:2075530/1‑91 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt > 1:2804467/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTATTTa > 1:3064575/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 1:1280170/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:223364/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:2080267/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 1:368310/91‑1 (MQ=255) aTACACTGGTCGTCATAATAAATCTATCTATTCAACTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTGTATTACTTAt < 2:2507239/91‑1 (MQ=255) aTACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAt > 1:973745/1‑91 (MQ=255) tACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAtt > 1:3107725/1‑91 (MQ=255) acacTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAttt > 2:3429936/1‑91 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3577849/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 1:1401461/1‑91 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 2:3564638/1‑91 (MQ=255) gCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtttt < 1:3626772/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 1:1712957/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:2417565/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:900542/91‑1 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat > 1:2586797/1‑91 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:80596/91‑1 (MQ=255) cGTCATAATAAATATATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:548778/91‑1 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 1:721085/1‑91 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 2:18470/91‑1 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 1:904672/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca > 1:1466094/1‑91 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca < 2:1394273/91‑1 (MQ=255) taataaATCTATCTATTCAAACATAAATAAAAGTTACCTACTCCATTCTATGTAGCCGGCAACCTTTATTTCTTATCACTTTtcattatcc > 2:1717946/1‑90 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt < 1:3860062/91‑1 (MQ=255) taaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatta < 1:1362140/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa > 1:1879843/1‑91 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa < 2:2916428/91‑1 (MQ=255) aaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAg < 2:3614580/91‑1 (MQ=255) atctatctATTCTAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACCTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3292364/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:1677655/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 1:2611178/91‑1 (MQ=255) ctatctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATGATCATTAAGTAc < 1:3027516/91‑1 (MQ=255) tatctatTCAAATATAAATAAAAGTTACCTACTACATTTTCTGTAACCAGCAACAGTTATTAATTATCTTTTTTCATTATCATTAAGTACt > 2:3675373/1‑91 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtt > 1:3241291/1‑91 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtt > 1:1918300/1‑91 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtt > 2:2358491/1‑91 (MQ=255) tctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACttt > 2:547590/1‑91 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3703108/91‑1 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt > 1:288295/1‑91 (MQ=255) ctatTCAAATATAAAAGAACGTTACCTACTACGTGCTATGTAGCAGGCCACTTTTATTACTTATTTCTTTTCATTATCAGTAAGTACtttt < 2:1100531/91‑1 (MQ=255) tatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa < 1:3085330/91‑1 (MQ=255) tatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa < 1:2962646/91‑1 (MQ=255) tatTCAAATATAAATAAAAGTTACATACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTa < 2:3685667/91‑1 (MQ=255) ttCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACa < 2:1260039/91‑1 (MQ=255) atatAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACtt > 1:1790012/1‑91 (MQ=255) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:2664347/4‑91 (MQ=14) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:3795675/4‑91 (MQ=14) taaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac < 1:1618282/91‑1 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCCCAt > 1:1032296/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt < 1:2127058/91‑1 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAATTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3538538/1‑91 (MQ=255) aaaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAt > 2:3492788/1‑91 (MQ=255) aaaGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTACCATTAAGTACTTTTACAAACTTCCCATTAtg > 2:1343929/1‑91 (MQ=18) aaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtg > 1:1813722/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt < 1:3448263/91‑1 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt < 1:3348634/91‑1 (MQ=255) aGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgtg < 2:1799748/91‑1 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt > 1:2847437/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt < 2:151119/91‑1 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAACCTTCACATTATGTGTCtt > 2:795858/1‑91 (MQ=255) | TCATTAATACAAGTCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTT > USA300TCH1516_ALE/2129278‑2129458 |
| 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: ‑ |