Identifying degenerate positions in Mus
Entering edit mode
6.3 years ago
Brice Sarver ★ 3.6k

Hi everyone,

Many exome studies perform analyses on subsets consisting of 0-fold, 2-fold, and 4-fold degenerate sites. It seems that studies either 1) use Sanger-sequenced amplicons and identify such site classes manually or 2) fail to mention specifics of how data were subset. It's done frequently in mouse and other model systems, so there must be an easy way to filter/subset on such sites without writing something from scratch.

I am wondering if something like a list of the coordinates of these positions exists for Mus (mm10). I haven't had any luck tracking down solid leads from papers, Biostars, or SEQanswers as of yet, though perhaps I'm searching for the wrong things. Any help is greatly appreciated!

EDIT: It appears that I can get a list of SNPs that are classified according to their "consequence type" from BioMart via querying the MM short variation database. This will also export the chromosome and position. Still interested in whether or not this will get me what I want or if there are other resources available.

Mus synonymous nonsynonymous genome degenerate • 1.6k views

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