sammyjava
commented
5 months ago I think I need a full mock-up of what you want. For one thing, GWAS do not have QTLs - they have marker-trait associations. The only thing that connects QTL Studies with GWAS is the use of the same markers, which may be associated with a QTL in a QTL study (and a trait via the QTL) or associated directly with a trait in a GWAS.
That being said, I'm happy to update what is shown in tables, on the Manhattan plot, and on the linkage group diagrams if I can see an example.
The Glycinemine report for a GWAS QTL paper only presents the GWAS QTL name used in the paper. Example: https://mines.legumeinfo.org/glycinemine/report.do?id=305000008&trail=%7c305000008. It does not display the QTL name used in the GWAS map. This name could be listed in the table that reports the paper's name for the QTL and the p-Value. The map name should also be included in the mouseover on each dot on the manhattan plot at the top of the page. When you click on a dot on the manhattan plot, you get a report for the "marker" but it also does not include the GWAS map name of the marker. Example: https://mines.legumeinfo.org/glycinemine/report.do?id=329000031. The JBrowse glyph for the marker uses the paper identifier of the marker. When you click on that glyph you are presented with details about the marker which really should include the GWAS map name. There should be a link to the GWAS map for each GWAS QTL name used. This would allow the user to to easily go between the physical map and the genetic maps in CMapJS. @sammyjava @StevenCannon-USDA @jd-campbell