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Table 2 SNP genotyping and filtering statistics

From: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

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
  1. aMinor allele frequency >0.01
  2. bRemoval of SNPs identified as being of poor quality as defined by the International Sheep Genome Consortium HapMap project [11]
  3. cRemoval of SNPs on the sex chromosomes
  4. dRemoval of one SNPs from each pair where r 2 > 0.05 within 50 SNP blocks