With advancements in next-generation sequencing technology, whole genome re-sequencing (WGS) has become the most rapid and effective method to identify the genetic variations in individuals of the same species or between related species. The variation information such as single nucleotide polymorphism (SNP), insertion and deletion (InDel), copy number variation (CNV), and structural variation (SV) obtained through re-sequencing is used in population genetics research and genome-wide association studies (GWAS). These powerful tools are used to investigate the causes of diseases, to select plants and animals in agricultural breeding programs, and to identify common genetic variations among populations.