Sunday, June 1, 2014

Genome Mate: Chromosome Map Segments

Chromosome Map Segments are a visual representation of the DNA segments that have been mapped to common ancestors.   It happens automatically when sufficient data has been added to Genome Mate.


 The Basics

This section will provide the information required to get the chromosome map at the top of the page to display.  It requires three sets of data:

  1. Family History File:  Profiles > Select Profile Name > Load Gedcom File > Select filename > Select the name of the profile person listed in the Gedcom > Yes
  2. Identify Segment Source:  Each chromosome is made up of one part paternal DNA and one part maternal DNA so the chromosome map segment must be identified as having come from your father or your mother.
  3. Identify Common Ancestors:   For the relatives on the DNA segment in question, identify common ancestors.
With these three pieces of information, the chromosome map segment can be created:
  • In Genome Mate > Click relative's match on the main page to open the match details page > Select ICW Group (M or P) > Select Confirmed Paternal > Select Confirmed Maternal > OK
Genome Mate will automatically create a temporary map segment for the match identified. If you change it, it will be automatically changed.  I use temporary segments to track a possible origin of a DNA segment when I find a common ancestor with one relative but have yet to triangulate it with another.

Some useful shortcuts:
On the chromosome map at the top of the page:
  • Left click on a segment to see all of the matches overlapping that segment
  • Right click to see what relative or relatives were the source of the segment and possible segment surnames

Working With Map Segments

The information contained in this section is entirely optional and not required for either the application or the chromosome map to work correctly.

Segment List:  On main page, Select Segments

The Segment List displays the paternal and maternal map segments that have been defined using the criteria discussed in the previous section. For each chromosome, the map segments are layered by the generational distance from the profile person.  In other words, a father's segments would be plotted first then overlayed with the grandfather or grandmother's segments and so on.  To see an individual layer, click on the generation's color in the lower right hand corner.

Export permanent map segment data by clicking on the CSV File button.

There are cases where manually adding a segment may be desirable.  For example, I have a very well defined section of DNA that is associated with my Native American heritage but zero matches on that section so I added a segment manually as a note to myself.  Using the Add Segment button will create a permanent segment in the generation specified.

Smaller map segments can also be filtered out by the Minimum Segment Overlap value set in Options.  Check the Hide Segments box to do so.

Right Click on Map Segment to View Description
Open a description of the Map Segment by right clicking on one of the segments on the map or optionally changing to a table view and selecting the segment.

The Segment Id is assigned automatically using either M for maternal or P for paternal plus the chromosome and the segment start point.  Information on the segment, the relative or relatives whose match created the map segment and the surnames associated with the MRCA are listed. 

To make this a permanent segment, click Save.  Additional documentation will be retained if added to permanent segments.

There is also the option to Mark  or set the ICW group of all segments whose start and end points fall within the map segment's range to the Segment Id.  For a relative's match to be marked, it must be on the same side of the family as indicated by an M or P in the first position of its ICW group.  This is used to filter surnames on the Match Detail page.

Not shown is the Delete button that is available when a segment is permanent.  Use this to remove unwanted segments but be aware that a temporary segment may replace it, if the underlying data has not been corrected.

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