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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

From: Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence and standard benchmark datasets

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