Table 2.

SNP genotyping and filtering statistics

Statistics	Welsh data set	Combined data set
SNPs genotyped	51,135	51,135
MAFa	50,741	51,036
HapMap quality filterb	48,640	48,935
Autosomal SNPsc	46,266	46,561
LD prunedd	11,527	25,254

^aMinor allele frequency >0.01

^bRemoval of SNPs identified as being of poor quality as defined by the International Sheep Genome Consortium HapMap project [11]

^cRemoval of SNPs on the sex chromosomes

^dRemoval of one SNPs from each pair where r ² > 0.05 within 50 SNP blocks