If your ArrayStar “Variants” project involves a SeqMan NGen .assembly that utilized both a VCF file (for SNPs) and a BED or manifest file (to specify targeted regions), SNPs located outside the targeted region(s) may not initially be visible when you view the SNP Table in ArrayStar. This is true even if you changed Targeted regions to Entire genome during ArrayStar’s Set Up Preprocessing step.
The reason is that, for assemblies that used BED or manifest files, the SNP Table initially shows only SNPs within the targeted region. In other words, the Show tool at the upper left corner of the SNP Table is set, by default, to Showing SeqMan NGen default SNPs.
If you would like to view all SNPs, including those outside the targeted region(s), simply click the small black arrow to the right of the Show tool and choose Show All SNPs.