Clicking on SNPs located in the “Graphic display” for the reference mRNA model, shows most of the SNPs to be introns, yet the graphic shows them all as coding. Why?
The problem appears to be that the results of the two mapping pipelines for the SNPs didn’t agree. One pipeline maps the SNPs to the genome (results are shown in the Reference Cluster Report), while the other pipeline maps the SNPs to the mRNA (results are shown in the mRNA graphic display). Although such a case is rare, it appears that some of the genomic SNPs (ie. rs2534719) map at the exon/intron boundary, and can therefore be classified as intron or exon depending on whether they map to the genome or the mRNA.
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