This Help document answers the following questions about the Mouse SNP summary:
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 - 999999999 bp
- Selected Strains: ALL
- Sorted by genome location
Showing markers 1 - 100 of 377269.
No. SNPs are not associated with markers of type QTL.
In the column headings of the summary report:
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.
You can filter results by dbSNP Function Class. Function Classes are assigned by dbSNP. Click here for a description of the dbSNP Function Classes. Click the "Filter SNPs by: dbSNP Function Class" button above your results and check the classes you wish to retain after filtering. 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.
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.