Hi Weizi, I guess "alternate assembly" is too broad of a term. We include several _hap sequences in our reference database and consider them to be part of the reference assembly because they are from NCBI's human build 36.
I see it as a flaw that our multiple mapping detector flags single mappings to chr6 and chr6_*_hap* as multiple mappings, and I will try to address that in future releases. Yes, if exception appears as "n/a" in a Table Browser joining query on snp130 and snp130Exceptions, that means that snp130Exceptions has no rows for that SNP (only snp130) -- it is mapped to the reference genome (including several haplotype assemblies from NCBI36) and we find no unusual properties. Hope that helps, and send as many questions as you have to [email protected], Angie ----- "Weizi Huang" <[email protected]> wrote: > From: "Weizi Huang" <[email protected]> > To: [email protected] > Sent: Friday, August 28, 2009 2:05:11 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Precise meaning of exceptions in snp130Exceptions table > > 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 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
