| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 870,161 | G→T | 12.9% | intergenic (‑199/+155) | USA300HOU_RS04240 ← / ← USA300HOU_RS04250 | hypothetical protein/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 870,161 | 0 | G | T | 12.9% | 106.4 / 2.2 | 41 | intergenic (‑199/+155) | USA300HOU_RS04240/USA300HOU_RS04250 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (14/21); new base T (4/2); total (18/23) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.77e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
CAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTAA > USA300TCH1516_ALE/870028‑870296 | cAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGCTTTTcc > 2:373063/1‑141 (MQ=255) cTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACgggg < 2:101772/141‑1 (MQ=255) tttAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTTCATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGa < 2:365798/141‑1 (MQ=255) aaTACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTg < 1:286943/141‑1 (MQ=255) aTACCGGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGa < 2:56996/141‑1 (MQ=255) aTACCAGTTCCCATCAATGCTTGTTAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGa < 2:147408/141‑1 (MQ=255) ccAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTCTGGCACGGGGACTGAttt > 2:261236/1‑141 (MQ=255) cggTTCCCATCAATCCTTTTGAATCTTTACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTc < 2:338498/139‑1 (MQ=255) aTCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAacac > 1:116077/1‑141 (MQ=255) tgttAAACTTTACCTTGTACGTTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAaca < 2:242030/141‑1 (MQ=255) tgtgAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGGCTGATTTCTTTACCACCATTAAaca > 1:108013/1‑141 (MQ=255) tgAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAAcaca < 1:238749/141‑1 (MQ=255) aCTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGCtt > 1:194450/1‑141 (MQ=255) aCTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGAtt > 2:225152/1‑141 (MQ=255) ccTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTTTTGTTCGTGGCCTCTTTTCTTTTCCTCCATTTAAGACAGCTtttttat > 2:303391/1‑141 (MQ=255) ttGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATtttttattt < 1:212689/141‑1 (MQ=255) ttCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTCTTTATTTTTAATCAt < 1:186515/141‑1 (MQ=255) ttCCACATTTAGCCTCTTCTTATTTTAATGCATTATTCAATGCGGGATTTACAAATTAATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCAt < 1:5268/141‑1 (MQ=255) tCCCCATGTAGCCTCTTCTTGTTTTAATGCATAATTCAATGCGGGATTTACAAATTTATCCCGTCTTTTTTTTGTGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATa > 1:267748/1‑141 (MQ=255) cATGTGGCCTCTTCTTGTTTTAATGCAGTATGCAATGCGGTATTTAAAGATTTATCACATCTTTTTTTTATTATTTTCACGCGGGTGCACGTTGGTCTTCAAAAGAGTTAAAGACAGATTTTTTATGTTTAAACATAGCtt < 2:78718/141‑1 (MQ=255) ccTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTa < 1:151789/141‑1 (MQ=255) ccTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCAGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATCGTa > 2:26926/1‑141 (MQ=255) ctctTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTGATTTTTCGGCACGGGGACTGAATTCTTTAACACCTTTAAACACTGATTTTTTATTTTTAATCATAGCTTTTTCGTAt > 2:46227/1‑141 (MQ=255) ctctTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTAt < 2:61202/141‑1 (MQ=255) cttGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGt < 2:365144/141‑1 (MQ=255) ttttAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTGAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGc < 1:331077/141‑1 (MQ=255) attattCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTTTTTTTTTCCAGCACGGGGACGGATTTCTTTAACACCTTTGGACACGGAGTTTTTATTTGTGATCTTAGCTTTTTATTATCATGTTTGTTAAGCtatg > 2:362528/1‑140 (MQ=255) attattCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCtata > 1:300923/1‑141 (MQ=255) ttCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCAAGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTttaaata > 2:118992/1‑141 (MQ=255) aTGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGTGTTCTTATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTc < 2:248976/141‑1 (MQ=255) tGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGtaa > 1:218268/1‑139 (MQ=255) gCGGGATTTCCAAATTTCTCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAg < 1:66111/141‑1 (MQ=255) cGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACCCCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTCGCTAAGCTATAAATAAGTCAGt > 2:50587/1‑141 (MQ=255) cGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGt < 2:15473/141‑1 (MQ=255) gATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTtc > 2:220687/1‑141 (MQ=255) cAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTaaa > 1:211952/1‑141 (MQ=255) tCTTTTTTTTATTATTTCCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTg < 1:46227/141‑1 (MQ=255) tCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTg < 1:338205/141‑1 (MQ=255) cTTTTTTTTTTTTTTTTCCGGCACGGGGACTGATTTCTTTAACACCCTTATACACAGATTTTTTATTTTTAATCATCGCTTCTTAGTATCCTGTTGGCTTATCTTTAAATCATTCAGTTTCTCTCAAAATTAAATCAcccc > 2:36941/1‑138 (MQ=255) tttttATGATTTTCCGGCATGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGt < 1:238059/141‑1 (MQ=255) tttATGATTTTCCGGCACGGGGACTGATTTCTTTTTCACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTaa < 1:348566/141‑1 (MQ=255) | CAGTAGAATCTTTAATACCAGTTCCCATCAATGCTTGTGAAACTTGACCTTGTACATTTCCCCATGTAGCCTCTTCTTGTTTTAATGCATTATTCAATGCGGGATTTACAAATTTATCCCATCTTTTTTTTATGATTTTCCGGCACGGGGACTGATTTCTTTAACACCATTAAACACAGATTTTTTATTTTTAATCATAGCTTTATAGTATCATGTTGGCTAAGCTATAAATAAGTCAGTTTCTCTAAAAATTAAATAACTGAATGTAA > USA300TCH1516_ALE/870028‑870296 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |