An important source of genome sequence variations, structural variants (SVs), are largely ignored due to the difficulty to precisely calling these variants. In this study, we used whole genome sequence (WGS) data to capture the SVs in various breeds. We have identified 84,561 SVs in 567 WGS animals. When compared the called SVs with the major quantitative trait locus for mastitis resistance on chromosome 6 near to GC gene, we found a duplication (DUP) is highly similar to previous reported copy number variant. Even though the linkage disequilibrium between the lead SNP for mastitis resistance and the called DUP is not complete, the SVs profile we obtained still showed the potential for identifying functional variants.