Whole genome sequencing of two Holstein cattle

In this study, we generated whole genome sequencing data from two Holstein cows using Lung tissue. Overall design: The lung DNA samples of the two Holstein cows were sequenced using the Illumina NextSeq550 platform, with the Nextera library preparation and sequence generation according to the manufacturer's protocols. NGSQCToolkit v2.3.3 was used to trimmed adapter sequences and low quality reads. All the clean reads were mapped on the reference genome (ARS-UCD1.2) using BWA v0.7.12 software. We only used the reliable mapped reads for SNP calling. The SNP positions within the aligned reads compared to the reference genome were detected using the pileup function in SAMtools v.1.7 utilities. SNPs were predicted with a minimum mapping quality (-Q) of 20 and with the minimum and maximum read depths of 3 and 100, respectively.