SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium

Table 2 Numbers of SNP pairs for which r² values were computed for the pig data

Number of pairs of SNPs	Allele counts
Possibly > 0.99	9,898,092
< 0.99 (partial sums)	6,179,862
Computed \(r^{2}\) values	3,718,230
Percentage (all SNPs)^a	0.27
Percentage (after pruning for complete LD)^b	0.31

^aNumber of computed \(r^{2}\) values as percentage of the total number of r² values
^bNumber of computed \(r^{2}\) values as percentage of the total number of r² values after pruning for complete LD

ISSN: 1297-9686