Are there any refSNP fields that indicate which SNP allele matches the reference genome sequence upon which the SNP was mapped?
We maintain the contig variant in one of our database tables, called SNPContigLoc, which is located in the organism_data directory of your organism’s database. Once you locate the organism_data directory (the previous link is to the human_9606 directory as an example), download SNPContigLoc.bcp.gz. The first column of this table is snp_id. The last column of this table contains the contig form of the variation (in SNP orientation rather than in contig orientation). When the orientation in the next to the last column of this table is set to one, you’ll have to reverse complement if you want the contig orientation.
Related Questions
- What do I do if my practice is outside the United States and has a different address than the fields indicate on my Options screen or the Patient Details screen for my patients addresses?
- How do I get the chromosome, chromosome position, alleles and Ancestral allele for each SNP in a file of refSNP numbers I obtained from HapMap?
- I can’t see a reference sequence in the IGV (Illumina Genome Viewer) or ICB (Illumina Chromosome Browser). How can I display a reference sequence?
