Genotyping of 123,898 non-redundant SVs in 95 Chinese cattle

Genotyping of the 123,898 nonredundant SVs was performed in 95 cattle that had been sequenced with short paired-end reads. Reads from all short-read sequencing datasets were mapped to the Mongolian_v1 reference. Mapping was performed by BWA-MEM (v.0.7.13-r1126) with default parameters. We used Paragraph (v.2.4a) to genotype the combined SVs using short-read sequencing data. BCFtools (v.1.9) was used to combine the results for all genotypes. Then, we replaced all the unfiltered genotypes in Paragraph with missing genotypes (./.) and excluded SVs without any remaining nonreference genotypes. To obtain a high-quality dataset of genotyped SVs, we removed the SVs that were genotyped in less than 80% of cattle.