Interpreting a Mouse SNP Summary
Interpreting a Mouse SNP Summary
This Help document answers the following questions about the Mouse SNP summary:
See also:
The Mouse SNP summary provides a general description of each Mouse SNP that your query returns. The page contains:
- You Searched for...
- Genome Region: Chr2:125618205 - 127618205 bp
- Selected Strains: ALL
- Sorted by genome location
Showing markers 1 - 100 of 46717.
No. SNPs are not associated with markers of type QTL.
There are several ways to use the summary reports. You can:
Results are sorted by chromosome and then coordinate value. See Interpreting the MGI Mouse SNPs Results Table for details about the data appearing in the table columns and rows.
Yes, you can.
Yes. You can drag strain and other column headings at the top of the results table to rearrange them.
When you search by for SNPs with the Search by Region tab, a SNP Density Heatmap appears above the Results Table. Each cell in the Heatmap represents 1/20th of the search region. Colors represent the relative SNP density across the sub-regions and range from white, for no SNPs in that region, to light blue for one SNP, to purple, to dark red for tens of thousands and more SNPs. Click on a cell to refine your search to that sub-region. Once you click on a cell, a link appears beneath the Heatmap that allows you to "Return to original search boundary."
You can filter results by SNP Function Class, and if you have selected a reference strain, Allele Agreement. Function Classes are assigned by dbSNP. Click here for a description of the dbSNP Function Classes. Click the "Filter SNPs by: Function Class" button above your results and check the classes you wish to retain after filtering.
For Allele Agreement, you have two options:
If you have reordered columns, filtering will reset to the original order.
In your search results, click on the SNPs to Text File icon. Your web browser will download a file of the results that remain after any filtering you may have performed, up to a 100,000 limit.
When there is genome coordinate discrepancy, the summary section with links to associated genes from any returned coordinate regions does not appear. When the discrepancy exists, a message indicating that the Associated Genes section is temporarily disabled appears in the query summary report and you cannot click either the MGI Mouse Genome Browser or the MGI genes/markers links to view any returned coordinate ranges. 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 39 but the dbSNP data references NCBI build 38). See Understanding Mouse SNP Coordinate Discrepancies for further information.