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Table 4 Number of computed r2 values in the simulated sequence dataset using PLINK

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

Window size

Step size

Number of computed r2 valuesa

50

5

2.65 × 109

500

50

2.70 × 1010

5000

500

2.70 × 1011

5000

5000

2.70 × 1012

500,000

50,000

2.70 × 1013

5,000,000

500,000

2.70 × 1014

  1. aComputed as \(\left( {10,812,225/ss} \right) \times \left( {ws^{2} - ws} \right)/2\), where 10,812,225 is the total number of SNPs, \(ss\) is the step size (i.e. the size of the shift of the windows), and \(ws\) is the window size used
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Genetics Selection Evolution

ISSN: 1297-9686