I had three Illumina whole genome of a single species. Two from cotton and one from soybean. There is a reference genome from JGI which was isolated from rubber. I did a strict alignment to this reference and called SNPs separately as well as mpileup with GATK. This is a haploid species so I filtered SNPs by 10x-1000x coverage and 100% alternate and count. After filtering, I did get SNP around 800,000 for all. Two cotton seems to have fixed differences >800k against the reference (but exactly same between two cotton) and same for the soybean too. But when checked with soy vs cotton, >799k were same.This shows that cotton and soybean are similar and are very different from JGI rubber genome. I also checked few papers and found that the cotton and soybean pathogen remain in the same clade while rubber one in different. I was wondering if there are any other analyses that can be included in this type of study? I appreciate any suggestions.
