Mouse Strains in mm10/GRCm38 dbSNP 142?
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21 months ago

I am using the pre-built HiSat2 index for mm10 with the snps. Looking at the script the devs provide, I can see they are using SNPs from UCSC golden path. https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/snp142Common.txt.gz

However, I would like to know which strains are included for this release. I cannot find any documentation online from my searches. Should I assume it's the same strains used in the MGP?

hisat2 mm10 mouse dbsnp • 1.4k views
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Entering edit mode
21 months ago
igor 12k

The UCSC Genome Browser tracks are described in the Table Browser section. Specifically, snp142Common:

This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) — collectively Simple Nucleotide Polymorphisms — from dbSNP build 142, available from ftp.ncbi.nih.gov/snp Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete.

The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population.

Unlike MGP, which is a very defined sequencing project, dbSNP is a database that accepts submissions from anyone. Thus, there is no guarantee that it is limited to specific strains.

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