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Table 1 Number of animals and amount of SNPs excluded during the quality control procedure of the genotype data

From: Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

Breed   Excluded SNPs* Remaining SNPs
  N MAF < 0.05 SNP CR < 0.90 HWE Het. Total3  
AL1 403 3,828 2,358 39 1 6,820 45,268
SA1 318 4,155 2,358 45 2 7,140 44,946
   MAF < 0.15 SNP CR < 0.90 HWE Het. Total3  
LN1 81 10,321 2,358 54 156 13,436 38,650
NU1 54 16,013 2,379 21 242 19,233 32,853
TO1 53 15,388 2,362 63 870 19,233 32,863
BO1 67 13,282 2,374 17 185 16,438 35,648
BO2 61 11,562 55 81 471 15,029 37,057
CA2 48 9,508 147 33 689 13,272 38,814
RL2 66 4,695 57 52 274 7,980 44,106
  1. 1Canada, 2Australia, 3It was excluded 2,958 SNPs without chromosome number and/or position information or SNPs located in the sexual chromosomes. AL: Alpine, SA: Saanen, LN: LaMancha, NU: Nubian, TO: Toggenburg, BO: Boer, CA: Cashmere, RL: Rangeland; *some SNPs were excluded due to more than one criterion,, MAF = minor allele frequency; CR = call rate; HWE = χ 2 test for Hardy-Weinberg equilibrium (p-value < 10−6). Het: excess of heterozigosity (>0.15)