Hi Weizi, MultipleAlignments is assigned only when dbSNP has multiple mappings to the reference genome -- we ignore mappings to alternate assemblies.
Regarding "MultipleAlignments,MultipleAlignments": In the table snp130Exceptions, there is a separate row for each mapping of a multiply-aligned snp, so each multiply-aligned rs ID has at least two rows in snp130Exceptions. E.g. rs713 has 3 mappings, so 3 rows: chrX 153145901 153145902 rs713 MultipleAlignments chrX 153108783 153108784 rs713 MultipleAlignments chrX 153071653 153071654 rs713 MultipleAlignments Some part of our software might be collapsing those rows by ID and concatenating the exception field. Is it some kind of Table Browser query where you see MultipleAlignments,MultipleAlignments", or in a different tool? Hope that helps, and please write us at [email protected] if you have any other questions, Angie ----- "Weizi Huang" <[email protected]> wrote: > From: "Weizi Huang" <[email protected]> > To: [email protected] > Sent: Thursday, August 27, 2009 8:41:57 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Precise meaning of exceptions in snp130Exceptions table > > Dear UCSC genome browser team, > > ��� Could you please clarify my understanding in the term > "MultipleAlignments" in table hg18.snp130Exceptions. > �� > ��� My questions are: > > ����� 1. If a SNP is mapped uniquely to reference assembly as well > as > alternate assemblies, will the SNP be annotated with exception > "MultipleAlignments" ? > > ����� 2. How� does exceptions like > "MultipleAlignments,MultipleAlignment," arise? > > ��� Thank you for your help and time! > > Best regards, > > Weizi > ����� > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
