TABLE 1.

Non-monomorphic variants captured by different platforms in this study.

Variants	Infinium Global Screening Multi-Disease Array (GSA-MD) (N = 72)	0.4X ultra low-coverage whole-genome sequencing (ulcWGS) (N = 72)	30X hcWGS (N = 13)
Raw number of variants	759,993 (v2.0)	NA*	9,737,221 (nonmonomorphic)
	730,059 (v3.0)
Imputed number (nonmonomorphic)	11,430,960	11,673,829	9,737,221
Number of SNPs	10,157,732	10,384,933	7,351,799
Number of indels	1,264,727	1,280,217	2,240,753

Note. All variants post-imputation for GSA-MD and ulcWGS platforms were unfiltered, with the exception of monomorphic variants. Similarly, 30× hcWGS data generated by GATK pipelines included only nonmonomorphic variants. The number of SNPs and indels were estimated separately. NA*: The pipeline to process ulcWGS data did not generate raw genotype hard calls; instead, it calculated posterior genotype likelihood for all polymorphic sites in the reference panel, later refined by the imputation tool GLIMPSE 1.0.0.