Get SNPs not found in a Nipponbare

SNP discovery from a region not found in the Nipponbare reference genome

Region of interest: Pstol1 gene (chromosome 12, 15.46 mbps to 15.62 mbps) in the Kasalath genome.

After inputting these information and reference genome setting, the query will return a link that enables downloading of a CSV formatted file SNP x 3k RG accession matrix. Inspecting this downloaded SNP matrix, there were 1,125 SNP positions discovered within this region, while no SNPs (blanks) were seen using Nipponbare genome, as expected. Without the Kasalath reference information, variant discovery would be impossible using the Nipponbare reference genome. These SNP positions can now be further examined and surrounding sequences extracted for Pstol1 marker assay design.