dbSNP - ancestral_allele and gene_name data missing in SubSNP table
Posted in Ask the GATK team | Last updated on 2014-01-17 18:57:38


Comments (1)

Question on the dbSNP database. Looks like the SubSNP table is the only location for ancestral_allele and gene_name information for a given snp_id/subsnp_id. However, these fields in SubSNP are very sparsely populated. For example, if you search the dbSNP web page :

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs5

you can see the ancestral allele for rs5 is G. However, if you search snp_id=5 in the SubSNP table, both ancestral_allele and gene_name are null:

mysql> select gene_name,ancestral_allele from SubSNP where snp_id=5;
+-----------+------------------+
| gene_name | ancestral_allele |
+-----------+------------------+
|           |                  |
+-----------+------------------+
1 row in set (0.00 sec)

Can anyone explain this discrepancy or know where I can get ancestral_allele or gene_name if not in SubSNP directly ?


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