Dear Genome Browser team, ���� Thank you very much for your previous detailed explanations.
���� I still have some other questions: �� ��� 1. Some SNPs are uniquely mapped in reference genome, but they still labeled as "MultipleAllignments". ������� For example, rs1002187. For your convenience, the following is the output from UCSC table browser. chr6�������������������� 29583446 rs1002187 near-gene-3 MultipleAlignments,MultipleAlignments,MultipleAlignments, chr6_cox_hap1 930755����� rs1002187 near-gene-3 MultipleAlignments,MultipleAlignments,MultipleAlignments, chr6_qbl_hap2 732699����� rs1002187 near-gene-3 MultipleAlignments,MultipleAlignments,MultipleAlignments, ������ I checked the SNP in dbSNP,� and found that chr6_cox_hap1 and chr6_gbl_hap2 are from alt_assembly _3 and alt_assembly_4 respectively.� Could you tell me what is happening here? Did I interpret the output wrong? ��� 2.� Does other exception terms refer to reference genome only? Can I be confident that if a SNP has exception "n/a", then it is uniquely mapped to the reference genome and is problem free during mapping process? ���� Thank you again for your help! Best regards, Weizi On Fri 08/28/09 2:41 PM , Angie Hinrichs [email protected] sent: 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" wrote: > From: "Weizi Huang" > 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
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