Table 2. Descriptions of genotype categories.

Genotype categories		Genotype from SNP array
		00	01	11
Genotype from sequencing data	01	FP	TP, MG	GE
	11	FP	GE	TP, MG

*Notes: TP means sequencing SNPs with matched array genotypes (The true genotype with true positive SNPs); GE means false genotypes from sequencing data at the matched positive array sites (The false genotype with true positive SNPs); FP means false genotypes from sequencing data with negative array genotypes (the false genotype with false positive SNPs) and MG means the missing genotypes from sequencing data at the positive array sites.