False Positive Regions
These are the regions included in GDAT, and they are a compilation of those known to be around the centromere and other locations. These regions are not activated by default, and it is completely optional to either activate or leave them inactive.
To activate these areas, right click (Control-Click on Mac) on the blank area, and select "Set default false positives for this profile".
You can also use the data entry points at the bottom of the area to add your own custom areas.
Once populated, a right click (control click on Mac) will allow for deletions to occur if desired.
When active, segments that fall into these regions, or overlap these regions by at least a length of 5 base pairs, will have their "Side" value displayed in a yellow coloured text on the Chromosome view. Segments that have a significant amount outside of the False Positive Region will have their side value displayed in black.
Once populated, a right click (Control-Click on Mac) will show a menu that will allow you to:
Reset the defaults
Add the False Positive regions to the Chromosome Browser
Delete them from the Chromosome Browser if they have been added
Delete a single False Positive Region from the table,
Delete all False Posititive Regions
Export the displayed data to a .csv file.
Note: Adding FPR's to the chromosome tab will also add this "Relative" to your F8 view when viewing All Sources as an estimated 2nd cousins, sharing around 224cM of DNA with the profile.
Adding the False Positives to the Chromosome Browser will Add a "relative" with the name of "False_Positive_Region" with a side B and Group "FPR". These segments will also appear in black in the mini chromosome map at the top of the view, but are not able to be used as filters, but a hover over a segment will give the region both as a tool tip next to the mouse, and at the bottom of the screen.
Segments in the false positive regions are displayed, hidden, or deleted, on a profile by profile basis.
Read more about Centromere regions: https://isogg.org/wiki/Centromere
Read more about other regions: https://isogg.org/wiki/Identical_by_descent#Excess_IBD_sharing
While these regions do not change as a general rule, different companies have over time used different chips to process your DNA and so there may be some slight variations to these values.
The table on the left shows the current default list of FPR regions.
You may also discover that you can identify personal pile up regions, and these can be added to this sections manually if you choose by entering the desired chromosome number, start and end points and clicking add at the bottom of the FPR table.
Manually added FPRs can also be added to the Chromosome browser and will display in the same way as the default FPRs.