Mouse SNPs not found in dbSNP 142

[rocco.piazza]

Hello UCSC team,

I noticed that mouse SNPs such as rs30910803, rs29968550 and rs30022167 are reported as 'standard' SNP using the dbSNP 137 track, as SNP 'mapping to multiple genomic loci' in dbSNP 138 while apparently they disappeared from the dbSNP 142 track.
What's the reason for this behavior ? Could you please take a look into it ?

All the best,
Rocco Piazza

[Brian Lee]

Dear Rocco,

Thank you for using the UCSC Genome Browser and your question about the change in the display of some SNPs,  rs30910803, rs29968550 and rs30022167, between snp137, snp138, and snp142 in the mm10 mouse database.

The results you are seeing is in regard to the weight given to each of these SNPs between the different builds. The track hides SNPs with higher weights because they are less reliable.  In snp137 each of these had a weight of 1 and so they were visible, in later builds each of these were given a weight of 2 and they became filtered out of the display by default.

Please know on the Track Description page you can change the default filter to include SNPs that have a weight of 2 or even a weight of 3. In the following session link the filter on the snp138 and snp142 tracks has been increased to 2 so that you can find each of these items. 

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=mm10.snpWeight

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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