Table 8 GSA assays with a PPV = 1 based on concordance with the1KG Phase 3 data and the rWGS data. Data is binned by alternate allele frequency
Allele frequency bins | Total QC pass assays | Assays with PPV = 1; GSA versus 1KG and GSA versus rWGS | % left | % filtered |
|---|---|---|---|---|
0–0.1 | 17,454 | 3283 | 19 | 81 |
0.1–1 | 138,342 | 99,508 | 72 | 28 |
1–5 | 104,272 | 88,235 | 85 | 15 |
5–10 | 58,421 | 48,532 | 83 | 17 |
10–20 | 78,631 | 66,027 | 84 | 16 |
20–30 | 52,398 | 44,511 | 85 | 15 |
30–40 | 36,620 | 31,223 | 85 | 15 |
40–50 | 27,476 | 23,563 | 86 | 14 |
50–60 | 23,053 | 20,041 | 87 | 13 |
60–70 | 20,134 | 17,799 | 88 | 12 |
70–80 | 19,210 | 17,318 | 90 | 10 |
80–90 | 14,312 | 13,103 | 92 | 8 |
90–100 | 4023 | 3564 | 89 | 11 |
Total | 594,346 | 476,707 | Â | Â |