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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