Whole-genome sequencing and variants data of 304 indigenous goats from Southwest China

Indigenous goats exhibit strong adaptability to remote environments and provide a vital source of protein for residents in impoverished regions. Whole-genome sequencing (WGS) data can elucidate the economic traits of these goats. However, the limited genomic resources have constrained the functional dissection of advantageous traits and hampered the breeding process in goats. Here, we present a WGS dataset of 304 goat samples, from the Guizhou black (n = 104), Hezhang black (n = 100), and Tashi (n = 100) goat breeds. The dataset consists of 6.0 TB of paired-end sequences generated through the BGI-T7 sequencing platform. The data has an average sequencing depth of 7.5X, a mapping ratio of 97.0%, and genome coverage of 98.4%. Following the variant calling and hard filtration, a total of 27.13 million single nucleotide polymorphisms (SNPs) and 2.76 million insertions-deletions (InDels) were retained. To our knowledge, this is the largest goat WGS dataset from Southwest China, significantly enriching the global public genomic resources for the study of genetic diversity, environmental adaptations, and functional genes in goats.