This Help document answers the following questions about the Mouse SNP summary:
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:
- A Query Summary at the top listing your selections and any defaults from the Mouse SNP Query Form; for example, the strain(s) you chose to compare, the chromosome location(s), the starting and ending coordinates, the maximum number to display, and the output format.
- Links to Mouse Genome Browser and MGI Genes/Markers (if you query by marker range or genome coordinates)
Note: If no SNPs are returned, these links do not appear, even though there may be markers in your range.
- The former link lets you view SNPs within the coordinate range from your query in the MGI Mouse Genome Browser.
- The latter link takes you to the MGI Genes and Markers Query Results -- Summary where all MGI genes/markers within range appear, sorted by coordinates.
- A link to a legend (see Interpreting the MGI Mouse SNPs Legend) which decodes the data in the box below it).
- A table containing additional information about the Mouse SNPs matching your query.
- The table headings always include SNP ID, Map Position, and strain names.
- Other data to appear depends on items checked in the Output options section of the Mouse SNP Query Form.
- Data may include reference SNP orientation to the mouse genome, associated gene and dbSNP function class, number of ss assays, variation type, and an allele summary of all strains selected.
- An option to view all MGI genes or markers within the coordinate range from your query.
- The number of matching Mouse SNPs displayed in the report.
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:
- The dbSNP build number appears (in parentheses) at the top of the SNP ID column.
- The NCBI build number appears (in parentheses) at the top of the Map Position column.
How do I use a Mouse SNP summary?
There are several ways to use the summary reports. You can:
- Select and view details about individual SNPs at dbSNP (NCBI) or MPD (Mouse Phenome Database) or on the MGI SNP Detail page.
- Return to the query page and
- Increase or decrease the maximum number of items returned (for example, when the display limit is less than the number of matching SNPs found).
- Change the allele display mode (Same, Different, All).
- Add or change selected strains or the reference strain.
- Change the marker range (genome coordinate discrepancies have a less severe effect on marker range searches when the distance between your flanking markers increases).
- Click the Back button to return to the results of a previous query. Here you can modify that query and run it again, or you can click Reset to empty all fields, restore default values, and then requery.
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.
- If you want to retrieve those matches right now, click the link (i.e., ftp://firstname.lastname@example.org/queryResults).
- If you want to access your results later, copy or save the URL to the MGI FTP site and make a note of how long they will be retained. If you don't retrieve your results within 72 hours, you'll have to rerun this query.