| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,129,381 | T→A | 7.0% | intergenic (+214/+24) | 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 | 2,129,381 | 0 | T | A | 7.0% | 943.4 / 43.1 | 285 | intergenic (+214/+24) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| Reads supporting (aligned to +/- strand): ref base T (133/129); new base A (5/15); total (140/145) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.53e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 292 total aligned reads displayed.
TCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCA > USA300TCH1516_ALE/2129291‑2129471 | tCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCt > 1:388758/1‑91 (MQ=255) cTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTa < 1:1347522/91‑1 (MQ=255) gctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGc < 2:664314/90‑1 (MQ=255) ctACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCTAATATAAATAAAAGTTACCTACTACATTCTATGTAGCa > 2:1082473/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAg > 2:2425507/1‑91 (MQ=255) tACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCCATGTAGCAg > 2:825787/1‑91 (MQ=255) acacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTAAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAgg > 2:3474772/1‑91 (MQ=255) cacTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGc > 2:3367217/1‑91 (MQ=255) gcTCAAACAAGATTCATACACTGCACGGCATAATTATTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCa < 2:3906949/90‑1 (MQ=255) cAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACt < 1:3496187/91‑1 (MQ=255) cAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACt < 1:2612728/91‑1 (MQ=255) agaCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCGATGTAGCAGGCAACtt < 2:579948/89‑1 (MQ=255) aaaCAAGATTCATACACTGCACGTTATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtt < 2:3681269/91‑1 (MQ=255) aaaCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtt < 2:1201540/91‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt < 2:2818716/91‑1 (MQ=255) aCAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACtttt > 2:3843796/1‑91 (MQ=255) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 2:3194058/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:666673/91‑1 (MQ=18) cAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTtta < 1:307732/91‑1 (MQ=17) aaGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttat < 2:2749402/91‑1 (MQ=18) gATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattt < 1:970102/91‑2 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:145970/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTttattta < 1:104816/91‑3 (MQ=17) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 1:2126433/1‑91 (MQ=255) aTTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAc > 2:3131723/1‑91 (MQ=255) ttCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACt < 2:2375416/91‑1 (MQ=255) tCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACtt > 1:3370192/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAGTTa > 1:3064559/1‑91 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:2080213/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 2:1747434/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 1:1280170/91‑1 (MQ=255) cATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTa < 1:368310/91‑1 (MQ=255) aTACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAt < 1:1764193/91‑1 (MQ=255) tACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTAtt > 1:3107725/1‑91 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt > 1:234957/1‑91 (MQ=255) cTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtt < 1:3577849/91‑1 (MQ=255) tGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCttt > 1:1390055/1‑91 (MQ=255) gCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCtttt < 1:3626772/91‑1 (MQ=255) cACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtc < 2:900542/91‑1 (MQ=255) cGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:80596/91‑1 (MQ=255) cGTCATAATAAATATATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcat < 1:548778/91‑1 (MQ=255) gTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcatt > 2:2227526/1‑91 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 2:18315/91‑1 (MQ=255) ataataAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatc < 1:904672/91‑1 (MQ=255) taataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatca < 2:1394246/91‑1 (MQ=255) aataaACCTATCTATTCAAATATACATAAAAGTTACCTACTACAATCTATGTACCAGGCAACTTTTATTACTTATTTCTTTtcattatcat > 2:2559474/1‑91 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt > 2:1512833/1‑91 (MQ=255) ataaATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt > 2:2838577/1‑91 (MQ=255) ataaATCTATATATTAAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTtcattatcatt < 1:2768130/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa > 1:1879843/1‑91 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa < 2:2916428/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa < 1:943060/91‑1 (MQ=255) aaaTCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTaa < 1:489179/91‑1 (MQ=255) atctatctATTCTAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACCTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3292364/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:1677655/91‑1 (MQ=255) atctatctATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGt < 2:3409610/91‑1 (MQ=255) tctatctaTTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTa < 2:2351591/91‑1 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtt > 1:1918300/1‑91 (MQ=255) atctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACATTTATTACATAATTCTTTTCATTATCATTAAGTACtt > 1:1939100/1‑91 (MQ=255) ctatTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACtttt < 1:3703108/91‑1 (MQ=255) ttCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACa < 2:1602298/91‑1 (MQ=255) tCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACaa > 1:3294593/1‑91 (MQ=255) cAAATATAAATAAAAGTTACCTACTACATTCCCTGTAGCAGGCAACTTTTATTACTTATTTCTTTTCGCTATCATTAAGCACTTTTACaaa > 2:3022224/1‑91 (MQ=255) aaaTATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAAc < 1:2073622/91‑1 (MQ=255) tataAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTc > 1:3470191/1‑91 (MQ=255) tataAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTc > 2:1959771/1‑91 (MQ=255) agtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTca > 1:3795675/4‑91 (MQ=14) taaataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac < 1:711358/91‑1 (MQ=255) gtaataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTcac > 2:127367/3‑91 (MQ=17) aaataaaAGTTACCTCCTACATTCTATGTAGCAGGCAACTTTTATTACTTATTGCTTATCATTATCATGAAGTGCTTTTATAAACTTcacc > 2:3541576/1‑90 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3694442/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3608818/1‑91 (MQ=255) aataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTAATTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAt > 2:3538538/1‑91 (MQ=255) ataaaAGTTGCCTGCTACATAGAATGTAGTAGGTAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAtt > 2:1294717/1‑91 (MQ=17) ataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAtt > 1:3848444/1‑91 (MQ=255) ataaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACAtt < 2:1107779/91‑1 (MQ=255) taaaAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTa < 1:2985310/91‑1 (MQ=255) aaaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAt > 2:3492788/1‑91 (MQ=255) aaaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtg > 1:1813707/1‑91 (MQ=255) aaGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgt > 1:1649240/1‑91 (MQ=255) aGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTAtgtg > 1:2473740/1‑91 (MQ=255) ttACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTACTTCTTTTCATTTTCATTAAGTACTTTTACAAACTTCACATTATGTGTc > 2:50419/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCt > 1:2847437/1‑91 (MQ=255) tACCTACTACATTCTATGTAGCAGGCAAC‑TTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt < 2:1407892/91‑1 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:3212661/1‑91 (MQ=255) aCCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCtt > 1:2892634/1‑91 (MQ=255) ccTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTc > 2:362955/1‑91 (MQ=255) ccTACTACATGCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTACGTGTCTTc > 2:1701524/1‑91 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa > 2:2446039/1‑91 (MQ=255) tactacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCa < 1:2161272/91‑1 (MQ=255) ctacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAAt < 1:2596006/91‑1 (MQ=255) tacATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATc < 1:458417/91‑1 (MQ=255) aTTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGGCTTCCAATCAAc < 1:3048466/91‑1 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt < 1:3542244/91‑1 (MQ=255) tCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACtt < 1:1593470/91‑1 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc < 1:1506220/91‑1 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc > 1:1010619/1‑91 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc < 2:3375303/91‑1 (MQ=255) cTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTc < 1:821002/91‑1 (MQ=255) tATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCa > 1:3775748/1‑91 (MQ=255) | TCTTTACTCTACACTCAAACAAGATTCATACACTGCACGTCATAATAAATCTATCTATTCAAATATAAATAAAAGTTACCTACTACATTCTATGTAGCAGGCAACTTTTATTACTTATTTCTTTTCATTATCATTAAGTACTTTTACAAACTTCACATTATGTGTCTTCCAATCAACTTCA > USA300TCH1516_ALE/2129291‑2129471 |
| 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: ‑ |