Interpreting a Mouse SNP Summary
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This Help document answers the following questions about the Mouse SNP summary:

See also:

What's in a Mouse SNP summary?

The Mouse SNP summary provides a general description of each Mouse SNP that your query returns. The page contains:

Will QTLs show up in a Mouse SNP summary report?

No. SNPs are not associated with markers of type QTL.

How can I tell which database build I'm querying against?

In the Legend section of the summary report:

How do I use a Mouse SNP summary?

There are several ways to use the summary reports. You can:

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How do I interpret the legend?

Results are sorted by chromosome and then coordinate value. Chromosome transitions are marked by blank rows. See Interpreting the MGI Mouse SNPs Legend for details about the data appearing in the table columns and rows.

How does genome coordinate discrepancy affect my results?

When there is genome coordinate discrepancy, the summary section with links to associated genes from any returned coordinate regions does not appear. This is because genome coordinates for mouse genes and markers in MGI are derived from the current NCBI mouse genome build but the coordinates for mouse SNPs are derived from an earlier NCBI mouse genome build (as, for example, when MGI genome coordinates are derived from NCBI build 34 but the dbSNP data references NCBI build 33). See Understanding Mouse SNP Coordinate Discrepancies for further information.

I got a summary report with a "Link to Results on FTP Site" message. What do I do now?

The Mouse SNP Summary Report with the FTP link summarizes your query parameters at the top of the page and beneath this, lists the number of items that matched your query.

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