Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

BMC Genomics

Table 5 MNEc2M and MNEc670k variant mean and median alternate allele frequency

SNP Chip	Sample Split	Mean ALT Allele Frequency	Median ALT Allele Frequency
MNEc 2M Variants	WGS + SNP	0.2115920561	0.0975609756
	SNP Only	0.208498773	0.0900621118
	WGS Only	0.2313047405	0.1258278146
MNEc 670k Variants	WGS + SNP	0.267280485	0.1729559748
	SNP Only	0.2647029832	0.1682389937
	WGS Only	0.2836436744	0.1895424837

Average (mean and median) values for MNEc2M and MNEc670k arrays broken down by genotype information available from WGS, CHIP or WGS + CHIP

ISSN: 1471-2164