Hello Oskar,
"N" in the file "All SNPs in Personal Genomes" implies lack of information. The file has SNP data from the Southern African genomes as well as a lot of other published personal genomes. For the other personal genomes, we did not have the consensus calls at all locations (we just have the SNP locations and calls) and hence that lack of information is depicted by the base "N". For the Southern African genomes, the lack of information could be because of the method used e.g. genotyping does not give the consensus call on every location, or because we had no coverage on that location.
In the future, please send Galaxy questions / correspondence to one of the Galaxy mail lists ( galaxy-dev@bx.psu.edu, galaxy-user@bx.psu.edu, galaxy-bugs@bx.psu.edu ) instead of my personal email address.
Thanks!
On Oct 14, 2010, at 5:00 AM, Oskar Hallatschek wrote:
Dear Greg,
could you please let me know whether an entry "N" in the file "All SNPs in Personal Genomes" refers to an unidentifiable base, and why there are so many such entries in the displayed Genome.
many thanks, Oskar -- Oskar Hallatschek MPI for Dynamics and Self-Organization Biological Physics and Evolutionary Dynamics Bunsenstr. 10, D 37073 Goettingen phone: +49-551-5176-670 fax: +49-551-5176-669 e-mail: oskar.hallatschek@ds.mpg.de http://www.evo.ds.mpg.de/
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu