Table 7 Number of GSA assays and their relative percentages binned by alternate allele frequency in 1KG Phase 3 data
Alternate allele frequency bins (%) | All GSA assays and in 1KG | GSA pass QC and in 1KG | Percent assays that failed QC (%) |
|---|---|---|---|
0–0.1 | 17,830 | 17,454 | 2 |
0.1–1 | 148,959 | 138,342 | 7 |
1–5 | 113,374 | 104,272 | 8 |
5–10 | 63,688 | 58,421 | 8 |
10–20 | 84,729 | 78,631 | 7 |
20–30 | 56,601 | 52,398 | 7 |
30–40 | 39,684 | 36,620 | 8 |
40–50 | 30,095 | 27,476 | 9 |
50–60 | 25,078 | 23,053 | 8 |
60–70 | 21,944 | 20,134 | 8 |
70–80 | 20,866 | 19,210 | 8 |
80–90 | 15,612 | 14,312 | 8 |
90–100 | 4552 | 4023 | 12 |
Total | 643,012 | 594,346 | 8 |