Understanding Mouse SNP Coordinate Discrepancies
Understanding Mouse SNP Coordinate Discrepancies
This Help document answers the following questions about genome coordinate discrepancy on the Mouse SNP Query Form.
The discrepancy occurs when genome coordinates for mouse genes and markers in MGI are derived from the current mouse reference genome build but the coordinates for mouse SNPs are derived from an earlier build (as, for example, when MGI genome coordinates are derived from the most recent Genome Reference Consortium reference assembly (GRCm39) but the SNP coordinates are from GRCm38).
The discrepancy in genome coordinates between SNPs and MGI genes exists when the SNP data for the current reference genome assembly are not yet available or have not yet been updated in the public variation archives.
| Query Form Section | Field | Discrepancy Impact |
|---|---|---|
| Marker range | Genome coordinates | Marker Range function is disabled temporally, while a discrepancy exists in MGI between the genome build for mouse SNP coordinates and the genome build for mouse gene coordinates. |
| Marker range | Marker range | Marker Range function is disabled temporally, while a discrepancy exists in MGI between the genome build for mouse SNP coordinates and the genome build for mouse gene coordinates. |
| Associated genes | SNPs Located Near Genes | This summary section is disabled until coordinate data for SNPs are derived from the same genome build as coordinate data for MGI genes. |
When the discrepancy exists, information appears at the top of your Mouse SNPs Query Results -- Summary report, indicating that the mouse SNP genome coordinates derive from a different mouse genome build than the MGI genome coordinates.