Using Genome Mate (Add confirmed segments to chromosome map)

The previous article in this series is Using Genome Mate (Identify triangulated groups and confirm segments).

In following the steps that have been previously outlined, we now know how to identify triangulated groups and confirm the segments within a triangulated group. This post will show the steps to add these triangulated segments to our chromosome map.

In order to show the process for adding a triangulated segment to your chromosome map, I will use a hypothetical example to provide some background information. In this example, let’s pretend I have emailed both kit A and kit B from my last post, and have received back replies from each of them with information about their ancestral lines. I find out from the administrator of kit A that the test taker is the granddaughter of John Isaac Egbert and Eliza Jane Seaver, through their daughter, Martha Eliza Egbert. I find out from the administrator of kit B that the test taker is the second great granddaughter of John Isaac Egbert and Eliza Jane Seaver, through their son Franklin Isaac Egbert. Knowing that I am the great grandson of John Isaac Egbert and Eliza Jane Seaver, through their daughter, Matilda Jane Egbert, we can say it is extremely likely John and Eliza are the source of this shared segment I share with kit A and kit B, since all three of our ancestral lines trace back to this same couple as our most recent common ancestors (MRCA).

Now that we have triangulated the segments to the MRCA, I can confirm them in Genome Mate. To do so, and subsequently add the segments to my chromosome map, I click on one of the segment bars that I want to confirm, which brings up a details screen. [Note: In order to be able to confirm segments in Genome Mate, a GEDCOM file of the tester’s ancestors needs to have been previously imported to the tester’s Genome Mate profile. If you have not already done so, please see Adding A GEDCOM File To Genome Mate for instructions.]

Genome Mate Screen Shot 25

As highlighted by the red rectangle in the screenshot below, on the middle lefthand side of the details screen is a place where you can record the ICW Group of this matching segment. Although you can enter anything you like to identify your segments, you can make the greatest use of the Genome Mate tools by following the conventions suggested by the program.

As noted in my last post on identifying triangulated groups, a segment will match you on either the paternal side of your family, or the maternal side of your family, unless your parents are closely related (which you can determine by running a GEDmatch one to one comparison between them). Once you’ve identified the ancestor(s) who passed the triangulated segment down to you, the first thing you should do in the details screen is select the radio button for the corresponding side of your family line (paternal or maternal) for the ancestor(s) this segment is inherited from. [Note: If your parents are closely related, for now it is best to leave the ICW Group for the segment as the default question mark (?) and not confirm the segment, until further comparisons can be done to narrow down the source of this specific segment, as will be covered in a future post.]

Continuing with our example, as shown on my pedigree chart, John Isaac Egbert and Eliza Jane Seaver are on my maternal side of the family, so I select the Maternal radio button, placing the letter M in the ICW Group box. Once the Paternal or Maternal radio button is selected, two additional radio buttons will appear for Grand Father and Grand Mother. If you have identified from which grandparent’s line the ancestor(s) from which this segment is inherited are a part of, click the corresponding radio button (Grand Father or Grand Mother). If you have not yet identified from which grandparent’s line the ancestor(s) from which this segment is inherited are a part of, leave the Grand Father and Grand Mother radio buttons blank. In this example, I know John Isaac Egbert and Eliza Jane Seaver are on my maternal grandfather’s side of the family, so I select the Grand Father radio button, which then shows MGF in the ICW Group box.

Genome Mate Screen Shot 34

Once I’m done with my selection of Paternal or Maternal (and Grand Father or Grand Mother, if known), I go to the upper righthand corner as highlighted by the red rectangle. Here I can select via dropdown boxes the paternal most recent common ancestor (MRCA), and/or the maternal most recent common ancestor (MRCA), that I share with the test taker whose segment I’m confirming. In this example, I use the two dropdown boxes to select my Paternal MRCA of John Isaac Egbert and my Maternal MRCA of Eliza Jane Seaver.

Genome Mate Screen Shot 36

Before proceeding, it’s a good idea to get in the habit of checking to make sure the ICW Group and MRCAs are as you intended. If they are not, go back and redo your selections. After making sure everything is correct, click the Save button at the lower right to confirm the selections we have made for the segment.

Genome Mate Screen Shot 26

Clicking the Save button will take you back to the Genome Mate main window. You will see the segment is now colored, indicating the MRCA has been selected. The color is a function of how many generations back the MRCA is in your ancestral line. Looking at the chromosome map at the top of the screen, you will see that this segment has now been added on the lower bar (maternal side). The first letter of the ICW Group we selected on the details screen (P or M) determines which side the confirmed segment is added to. Since I selected MGF for this segment (to indicate my Maternal Grandfather, as it is this ancestral line the segment was passed down to me from), the confirmed segment is added to the maternal side of my chromosome map. Had the MRCA been from my paternal ancestral line, and I selected P for the ICW Group, the confirmed segment would have instead been added to the upper bar (paternal side) of my chromosome map.

Genome Mate Screen Shot 28

If I click on the Segments menu option (one of the selections on the line immediately below the chromosome map), I can see my entire chromosome map for all of my chromosomes and confirmed segments. As with the mini chromosome map that appears in the main Genome Mate screen, the segment we’ve confirmed appears on the lower bar (maternal side) of chromosome 2 in my full chromosome map. I can now go back and repeat the process to confirm the other segment I’ve identified the MRCA(s) for in this triangulation group.

Genome Mate Screen Shot 29

Congratulations, we have successfully worked through identifying a triangulated group and confirming a segment. This process gets repeated over and over as we work through all of our segments, attempting to identify the MRCA(s) for each one. As you continue to work through all your segments and triangulated groups using this process, and confirm which ancestor(s) the segments are inherited from, they will be added to your chromosome map, filling more and more of it in. Where they overlap, the confirmed segments of older generations will cover up the confirmed segments of younger generations. This allows you to pinpoint, with increasing precision, from which ancestor(s) a specific segment of DNA was inherited from.

In the next post, I will begin to demonstrate and explain some of the built-in tools Genome Mate has to make it easier to identify triangulated groups and confirm segments, and track your correspondence with matches. As with all my posts, if you experience any problems while following these steps, notice that a screen has changed dramatically from what I’ve shown in the screenshots, or have an easier/better way to do the steps shown, please let me know by commenting on this thread or sending me an email. Thank you.

The next article in this series is Using GEDmatch (The Triangulation Tool).

This article last updated 12 Mar 2015

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11 thoughts on “Using Genome Mate (Add confirmed segments to chromosome map)

  1. Pingback: Steps to DNA Matching and Chromosome Mapping Success with GEDmatch and Genome Mate | Adventures In Genealogy Research: No Stone Unturned/The Wright Stuff

  2. Pingback: Using GEDmatch (The Triangulation Tool) | Adventures In Genealogy Research: No Stone Unturned/The Wright Stuff

  3. Dan – I’m confused and need to be sure I am clicking in the correct place. You say “If I click on the Relatives menu option (one of the selections on the line immediately below the chromosome map), I can see my entire chromosome map for all of my chromosomes and confirmed segments.” When I do that I get a list of names, email addresses and GedMatch key numbers. If I click on “Segments” it seems to bring up the chromosome map. I’ve been tied up lately and haven’t had much time to play with Genome Mate but wanted to catch up with your more recent posts. Thanks so much for your work on this series.

  4. So far I have followed your directions and had no problems. Today, perhaps getting in a hurry, I tried to add confirmed segments to my chromosome map and clicked on the wrong person in my maternal line for MRCA
    Can I undo it? Thanks, Linda

    • Hi Linda,

      Sorry for taking so long to see your comment and reply. Yes, you can undo the confirmed segment by just selecting someone else and then saving again. If you want to remove the confirmation entirely, just select Paternal MRCA and Maternal MRCA (the first entry in both dropdown lists) and then save again.

      Best wishes,

      Dan

  5. I have located a match to my Mom through her father and then her father’s mother so I have clicked paternal and grandmother. I then added the MRCA’s but these MRCA’s are both her four and five times great grandparents via a first cousin, once removed marriage. The MRCA’s only show once in the list (although they are correctly attributed in the tree/gedcom) with a (7) but this match is at the MRCA’s closer level and should be (6). And is the color applied to the segment supposed to match the legend on the segment map? Also, let’s say I have six matches on Chr 1 with the MRCA’s being Mom’s 3 x’s ggs. Now I have another match in the same line but one generation further back on Chr 3 and some of those Chr 1 matches also match here. So I should assign the Chr 3 segment/Chr 3 matches to the 4 x’s ggs, correct? Not that I have a million matches, but I just went through and deleted all my segment information to start over and hopefully get it right this time. Thanks!

    • Hi RRD,

      Thanks for your questions. Closely related relatives marrying can certainly pose problems for the software to correctly reflect. Even though your ancestors are being attributed as generation seven, rather than six, due to the first cousin once removed marriage, there should be no harm in this. While, ideally, the color applied to the segment should match the legend on the segment map, I output a .csv file from Genome Mate and use this file with Kitty Cooper’s Chromosome Mapping Tool in order to have the greatest flexibility in how the output appears. When it becomes available, the new Genome Mate Pro looks like it may offer some more flexibility with the chromosome maps it generates. In regards to your last question, what I find works best is to take each segment individually, regardless of how that person may match on other chromosomes, and assign it the MRCA that corresponds in that situation. As you incorporate more and more data, you’ll start to see that some of your matches can match you on multiple lines, so the MRCAs between the segments they share with you will in fact be different. Hope this helps clear these things up a bit, but if not, please let me know.

      Best of luck on your research,

      Dan

      • Thank you! I do just have one more question…I think I understand what you’re saying about assigning the MRCA that corresponds in that situation but I would like to clarify that. So if I have third cousins that match on three chromosomes but I have no one else beyond that group to add to any of the three chromosomes, for now do I just designate the MRCA on each of the cousins’ records but not name any of those segments since it won’t let me use the same name for all three? Thank you so much!

    • Hi Double Karma,

      Thanks for your question. It can be tricky to work out which side a match connects with you on, and largely depends on how many known relatives have tested. For example, my paternal grandmother is still alive, so I had her take the test in addition to my dad. My maternal grandmother had passed away by the time I started using genealogical DNA testing, but one of her brothers was still alive at that time, so I had him take the test in addition to my mom. If it is not possible to test your grandparents or their siblings (either because they have passed away, or will not consent to taking the test), the next best thing is to test as many known cousins as you can. As you start working through your match list, and discover which of your known relatives these matches also share, you can begin fitting the pieces of the puzzle together. As another example, if I discover I have a match, who in turn also matches a couple of my known cousins who share one of my lines, then I know the shared connection with this new match is very likely to be along that same ancestral line of mine. The more comparisons you can do with known relatives, the easier and more specific the process becomes of determining which line the connection falls on.

      I hope this is of help, but if not, feel free to ask additional questions.

      Best wishes on your research,

      Dan

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