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.