Comprehensive Whole-Genome Variant Dataset from 711 Water Buffalo Samples Supporting Pangenome Analysis

This dataset supports the findings presented in the manuscript “A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection” (https://doi.org/10.1101/2025.05.04.652079). It comprises a globally representative cohort of whole-genome variant calls from 711 water buffalo samples, genotyped using PanGenie against the water buffalo pangenome. It offers a comprehensive variant panel, including short variants (single nucleotide variants) and long variants (structural variants), jointly characterized across this large-scale buffalo population. The dataset comprises 24 compressed VCF files each suffixed with *.vcf.gz, and corresponding to a single chromosome. Sample metadata is available in Supplementary Table S1 as cited in the manuscript. Additionally, an MD5 checksum file (md5sum_list.txt) is provided for user convenience.