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.

附加文件7 表S5：多等位基因变异体的数量与占比。多等位基因变异体的占比通过将多等位基因变异体数量除以非固定高质量变异体数量计算得到。当在VCFtools中设置‘-min-alleles 2 –max-alleles 2’参数标识时，即可识别出多等位基因变异体。等位基因不符合哈迪-温伯格（Hardy-Weinberg）平衡比例的变异体数量，指使用PLINK进行哈迪-温伯格平衡检验时，P值低于10^-8阈值的变异体数量。占比以括号标注形式给出。