Structural variation Analysis
Clipped, discordant, unmapped, and indel reads from each sample were used for structural variation analysis. The reads were collected from samples having GWAS significant SNPs with homozygous allele alternative (ALT) to the reference genome. Reads from each sample were grouped based on homozygous ALT alleles and assembled separately using spades software (SPAdes-3.15.2) (Bankevich et al., 2012). According to the manual recommended parameters, the mapping and annotation of structural variation from assembled contigs were performed using Assemblytics software (Nattestad & Schatz, 2016). Assembled contigs were aligned against the reference genome using nucmer software (Marçais et al., 2018). We then mapped structural variation breakpoints and annotated them using the Assemblytics software.