We submitted a new WGS dataset from three indigenous goat breeds, including Guizhou black goats (GBG, n=104), Hezhang black goats (HBG, n=100), and Tashi goats (TG, n=100), and there is the final SNP.vcf (27,134,128 SNPs) and InDel.vcf (2,762,642 InDels) files of the WGS dataset.