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Table 2 Number of autosomal SNPs excluded during the quality control procedure of autosomal SNPs

From: Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

Breed Excluded SNPs Remaining SNPsb
MAF < 0.05 SNP CR < 0.90 HWE p-value < 0.00001
Duroc 16,815 2,849 4,503 34,927
Landrace 10,136 2,849 1,251 42,164
Yorkshire 10,260 2,837 1,905 42,121
Crossbreda 10,934 2,593 1,756 42,325
  1. MAF minor allele frequency, CR call rate, HWE χ2-test for Hardy-Weinberg equilibrium, a: Landrace x Yorkshire, b: after exclusion of 608 possible misplaced SNPs