question about mouse SNP frequencies

[Oberdick, John]

Hello. I am browsing the UCSC mouse genome and have one simple question. Are the indicated population frequencies of various SNPs based on single individuals from the reference genome strain (C57BL/6), or is it based on sequence data from individual mice of multiple strains? That is to say the SNP frequencies appear to be based on percentages out of 30 individuals (T: 33.333% (10 / 30); C: 66.667% (20 / 30)..., etc). But I cannot find any indication of the strain composition of the 30 mice.

My larger question is how much SNP variation would one expect to see amongst individuals within an inbred strain? I assume the answer is very little. Thanks for your help here. -John Oberdick

John Oberdick, Associate Professor
Department of Neuroscience
The Ohio State University Wexner Medical Center
Co-Director, Neuroscience Graduate Studies Program
The Ohio State University
206 Rightmire
1060 Carmack Rd
Columbus, OH 43210
P: 614-292-8714
Fax: 614-292-5379
oberd...@osu.edu

[Matthew Speir]

Hi John,

Thank you for your question about the population frequencies for SNPs in the mouse genome. Unfortunately, we do not keep the population information when we import the data from dbSNP. However, you can get the population information for a particular SNP from its dbSNP's detail page, for example, http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs49332152. You can find a link to dbSNP's page from our details page for that SNP. After you've navigated to the dbSNP page, scroll down to the page to the "Population Diversity" section. For example, you can see that for the SNP rs49332152, the allele counts are reported for MM_PANEL2. Clicking the MM_PANEL2 link leads to the page: http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?pop=1445. This page lists 15 strains, meaning that 30 chromosomes are reflected in the allele counts. Unfortunately, UCSC does not have enough info to determine how much variation exists within the reference genome strain (C57BL/6).

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[Oberdick, John]

OK thank you very much. Have a happy new year! -John

John Oberdick, Associate Professor
Department of Neuroscience
The Ohio State University Wexner Medical Center
Co-Director, Neuroscience Graduate Studies Program
The Ohio State University
206 Rightmire
1060 Carmack Rd
Columbus, OH 43210
P: 614-292-8714
Fax: 614-292-5379
oberd...@osu.edu

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From: Matthew Speir [msp...@soe.ucsc.edu]
Sent: Monday, January 05, 2015 2:48 PM
To: Oberdick, John; gen...@soe.ucsc.edu
Subject: Re: [genome] question about mouse SNP frequencies