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Table 5 Number of pairs of SNPs for which r2 values were computed for the simulated sequence dataset

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

Number of pairs of SNPs

Phased alleles

Allele counts

Possibly > 0.99

107,576,540,902

107,567,702,834

< 0.99 (partial sums)

61,142,300,573

61,152,664,161

Computed \(r^{2}\) values

46,434,240,329

46,415,038,673

Percentage (all SNPs)a

0.08

0.08

Percentage (after pruning for complete LD)b

0.47

0.47

  1. aThe number of computed \(r^{2}\) values as percentage of the total number of r2 values
  2. bThe number of computed \(r^{2}\) values as percentage of the total number of r2 values after pruning for complete LD