One factor is that flanking sequences must be long enough to uniquely locate the reported snp via alignment. If it happens to be in a repetitive region the flanks may be longer.
On Dec 30, 2009, at 9:43 AM, Hiram Clawson <[email protected]> wrote: > Good Morning Kyle: > > I can't tell exactly why this is, and the person that would know > exactly is out of the office for the holidays. It looks like it > is a function of the type of the SNP. These sequences with their > fixed sizes appear to come from NCBI when we pick up the SNP data. > > Perhaps we can get a more definite answer for you in the New Year > when the office is back at full staff. > > --Hiram > > Kyle Tretina wrote: >> To whom it may concern, >> >> When I enter in an rs number that corresponds to a SNP in your >> database, >> what determines how much sequence upstream and downstream is pulled >> from the >> genome? For example rs34668160 yields 300bp upstream and 300bp >> downstream of >> the SNP, while rs12014875 yields 500bp upstream and 500bp >> downstream. What >> determines this? >> >> Kyle Tretina >> Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
