Hello Noboru, You may have missed this section on the SNP track description:
--- dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. --- Here are the counts of each class of in-del as they appear in the hg18.snp129 table: mysql> select distinct class, count(class) from snp129 where class='in-del' or class='insertion' or class='deletion' group by class; +-----------+--------------+ | class | count(class) | +-----------+--------------+ | in-del | 200655 | | insertion | 1672392 | | deletion | 1143502 | +-----------+--------------+ 3 rows in set (13.33 sec) Regarding the two SNPs you mention below that are not in the snp129 table: we use coordinates from dbSNP in the file b129_SNPContigLoc_36_3.bcp.gz and b129_SNPContigInfo_36_3.bcp.gz. If they are not present in that file, they will not appear in our table. I looked up the two SNPs at http://www.ncbi.nlm.nih.gov/SNP/, and it looks like neither of them were mapped to the genome by NCBI. On the page for rs36233812, I see: GeneView: no link established by analysis of contig annotation GeneView: no link established by BLAST analysis of mRNA sequences MapViewer: rs36233812 was not linked to the human genome 36.3 mapviewer. I hope this helps. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/18/09 18:31, Noboru Jo Sakabe wrote: > Hello, I am using table snp129 from Variants and Repeats in hg18 and > I have a question about in-dels. > The paper by Mills et al Genome Res. 2006. 16: 1182-1190 > http://genome.cshlp.org/content/16/9/1182.full identified 415,436 unique > INDEL polymorphisms that were deposited in dbSNP in 2006. > Why aren't they in UCSC's table snp129? I only found ~200,000 in the > file. (grep in-del snp129 | wc) and about 12 million SNPs, which seems > to be current with dbSNP. > Two examples are presented below, they are in current NCBI's dbSNP, > but not in file snp129 downloaded from UCSC. > > rs36233812 > rs36233828 > > Thanks for your help! > > Noboru > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
