How do you assign strand orientation to a refSNP (rs) in the MapLoc element (from the Primary Sequence element), and how is the “orient” attribute determined?
The “orient” value is determined by mapping SNP flanking sequences to a contig sequence using BLAST. Please note: a refSNP(rs) flanking sequence will never change orientation even if submitted SNPs in the opposite orientation are assigned to the refSNP (rs) cluster. Also, during a build, refSNP flanking sequences are BLASTed against contigs. If an rs maps to different contigs in each of two different builds, then the strand (or “orient” attribute) of the two different contigs to which the rs maps are in opposite orientation.
