Additional file 7 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Additional file 7 Table S5: Number and percentage of multiallelic variants. Percentage of multiallelic variants is obtained from the division of multiallelic variants to non-fixed high-quality variants. Multiallelic variants are identified when the ‘-min-alleles 2 –max-alleles 2‘ flag is set in VCFtools. Alleles not in Hardy-Weinberg proportions are the number of variants with P-value below the threshold of 10-8 when testing for Hardy-Weinberg proportions with PLINK. Percentages are between parentheses.