Additional file 3 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Additional file 3 Table S3: Number of variants during the different filtering steps: from original variants to high-quality and non-fixed variants. Original variants are considered as the raw variants retrieved from GATK. Low quality variants are discarded during hard-filtering and fixed variants are identified when the minor allele count (MAC) is set to 1 in VCFtools. The percentage of variants to the original variants before hard-filtering are in parentheses.