Is the trait/allele that was carried by the common ancestor of the taxon you consider.
I want the ancestral allele for a number of rsIDs, but can’t find rsID numbers in Allele.bcp.gz and SNPAncestralAllele.bcp.gz. If you go to the dbSNP Data Dictionary and search for “ SNPAncestralAllele ”, you’ll find that the rsID is stored as an integer in the first column of the table. Ancestral allele data is provided to dbSNP as part of the SNP assay data that is provided in dbSNP submissions, so we don't have a program that allows us to annotate ancestral alleles, and we don't currently have a mechanism for third party annotation of SNPs. You can the get ancestral state of each SNP (when this ancestral state is known) by using the following two tables from the FTP dump files:1.Go to the organism ​_shared_data file located in the dbSNP FTP site, and download the Allele.bcp.gz file. The ancestral alleles associated with the phase1 release where generated using two different processes. The snp ancestral alleles were derived from Ensembl Compara release 59. The alignments used to generate them can be found in the phase1/supporting directory. For example if you have in the populations the two following variants at the same locus: AGCCGT and AGCTGT, then you have a SNP at the position of the C and T. This type of variation is very common. We estimate that there are about 10 millions SNPs in the human genome. We often use these SNPs as genetic markers. Ancestral vs derived alleles. An ancestral allele or an ancestral trait (depending on whether you look at the phenotype or a t the genotype) is the trait/allele that was carried by the common ancestor of the taxon you consider. 2.You can also get the ancestral state of a SNP(when this ancestral state is known) by using the following 2 tables from the FTP dump files:a.Go to the organism ​_shared_data file located in the dbSNP FTPsite, and download the Allele.bcp.gz file.
http://www.ncbi.nlm.nih.gov/books/NBK44409/ http://www.ncbi.nlm.nih.gov/books/NBK44409/ http://www.ncbi.nlm.nih.gov/books/NBK44409/ http://www.1000genomes.org/faq/where-does-ancestral-allele-information-your-variants-come http://biology.stackexchange.com/questions/19159/ancestral-allele-explanation http://www.ncbi.nlm.nih.gov/books/NBK44409/
what is the ancestral allele