Hello, Oriane. dbSNP's strand is determined by the orientation of the submitted flanking sequences, so it is pretty arbitrary and has nothing to do with genes or other genomic features.
The allele frequencies should be consistent with the reported strand. The reference genome assembly was constructed from the sequences of a small number of individuals and does not always contain major alleles. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Oriane Sent: Monday, April 09, 2012 5:25 AM To: [email protected] Subject: [Genome] A/T SNPs Dear UCSC team, I'm a little bit confused about the data regarding the following A/T SNPs in the CNTN5 gene : rs3758923 rs1944169 rs1216183 - Why are these SNPs indicated on the minus strand, while the gene is in forward orientation ? - Are the allele frequencies given, those on the plus strand ? If not, how come that the "reference allele" is always the least frequent ? Thank you very much in advance. Regards, Oriane Mercati PhD student Institut Pasteur 25 rue du Docteur Roux 75724 Paris cedex 15 00 33 (0)1 45 68 88 04 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
