Skip to main content

Table 2 Number of SNPs on each simulated panel before and after quality control for imputation to 50K or 777K SNP panels 1

From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle

Commercial name Label Number of SNPs Number of SNPs in the imputation to 50K Number of SNPs in the imputation to 777K
Illumina Bovine3K 3K 2,900 2,321 2,359
Illumina BovineLD 6K 6,909 6,205 6,216
Beef LD GeneSeek Genomic Profiler 8K 8,762 7,033 7,478
15K panel2 15K 14,195 12,304 12,345
Indicus LD GeneSeek Genomic Profiler 20K 19,721 7,320 16,047
Illumina BovineSNP50 50K 54,609 43,247 43,247
GeneSeek Genomic Profiler Indicus HD 90iK 74,085 - 55,819
GeneSeek Genomic Profiler Beef HD 90tK 76,992 - 61,445
Illumina BovineHD 777K 787,799 - 587,620
  1. 1The SNP quality control included GenCall score (> = 0.15), Call Rate (> = 0.90), Hardy-Weinberg Equilibrium (P > =10−6), removal of non-autosomal chromosomes and SNPs not in common with reference panel;
  2. 2Non commercial panel. The 15K panel was created based on the Beef LD GeneSeek Genomic Profiler (8K) panel by expanding it with SNPs selected based on minor allele frequency greater than 0.23, linkage disequilibrium less than 0.088 and preferably located evenly spaced between two SNPs in the 8K SNP panel.