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(a)bx.psu.edu, galaxy-user(a)bx.psu.edu, galaxy-bugs(a)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(a)ds.mpg.de
http://www.evo.ds.mpg.de/
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu