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Table 5 Summary of GSA assays subgrouped by nucleotide variation type

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

Nucleotide variant type assay subsets

All GSA data

GSA pass manifest clusterfile QC

GSA pass manifest QC and present in 1KG Phase 3

Single nucleotide variants (SNVs)

656,601

606,524

594,230

Multi-allelic variants (MAVs)

616

526

3*

Insertions

1110

1044

36

Deletions

2799

2677

95

Total

661,126

610,771

594,361

  1. *Poor overlap with 1KG MAVs and excluded from further analysis