Skip to main content

Table 6 Distribution of GSA (reference (Ref) to alternate (Alt) allele) SNV assays present in the 1KG Phase 3 data versus number of assays passing QC

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

  Ref\Alt Purine Purine Pyrimidine Pyrimidine
A G C T
Purine A 101,994/111,493 (91%) 25,107/28,214 (89%) 1368/2065 (66%)
Purine G 136,350/149,635 (91%) 2404/3280 (73%) 29,629/33,115 (89%)
Pyrimidine C 30,130/33,566 (90%) 2339/3216 (73%) 136,392/149,801 (91%)
Pyrimidine T 1362/2074 (66%) 24,983/28,133 (89%) 102,172/112,009 (91%)