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

BMC Genomic Data

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

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

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;
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.

ISSN: 2730-6844