I am seeing some tracks on the December and October 2000 assemblies that have tracks for snpNIH overlap SNPs and snpTsc random SNPs. Where are these defined?
Response: Good question. While there is a page of terminology explanations, only the basic SNP is explained there: “SNP: Single necleotide polymorphism, or a single nucleotide position in the genomic sequence for which two or more alternative alleles are present at appreciable frequency (traditionally, at least 1%) in the human population.” On the center text line of the browser graphic, it explains that overlap SNPs come from clone overlaps. These SNPs might then be useful in confirming the assembly of putative overlaps or for being located in a largish section and so are broken out. For random SNPS, the center line says they are from random reads. The snpTSC stands for The SNP Consortium and NIH’s dbSNP; both random and overlap SNPs accessions start with an rs which is explained at the NIH site, eg rs792507. The dispersion of the two types of SNPS can be viewed anywhere in the browser. They are disjoint as sets but otherwise fully interdigitated. There are fewer overlap SNPS that sho
