Hi
I downloaded the the Table: snp132Common from Track: Common SNPs(132). A quick statistics is shown as below: #type of validation count by-1000genomes 4698898 by-2hit-2allele 1064881 by-cluster 3412491 by-frequency 2847474 by-hapmap 717332 by-submitter 138079 unknown 54311 I saw only 717332 from hapmap, while in Hapmap FTP site (ftp://ftp.ncbi.nlm.nih.gov/hapmap), I saw over 4 million SNPs. Why is there such a huge difference? Thanks Also, where could I found a more detailed README regarding those validation types, so that I can have a better idea of assess each type? Currently, I can only assume Hapmap and 1000Genomes are more reliable than the others. * Validation <http://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=validation> : Method used to validate the variant (each variant may be validated by more than one method) * By Frequency - at least one submitted SNP in cluster has frequency data submitted * By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method * By Submitter - at least one submitter SNP in cluster was validated by independent assay * By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes * By HapMap - submitted by HapMap <http://hapmap.ncbi.nlm.nih.gov/> project (human only) * By 1000Genomes - submitted by 1000Genomes <http://1000genomes.org/> project (human only) * Unknown - no validation has been reported for this variant Thanks Sean _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
