We split the genotypes from 5,129 distantly related CARe individuals into two groups. The common group contained those SNPs with MAF > 5% in both CEU and YRI. The uncommon group contained all other SNPs (i.e. MAF < 5% in either or both of CEU and YRI). The genotype kinship matrix K was constructed over the common SNPs and the local ancestry kinship matrix Kγ was constructed using the local ancestry called at every 5th common SNP.
