The Chromosome Browser: A Tool for Visualizing Segment Data
For most of us, the goal of genetic genealogy is to identify how our DNA matches are related to us. We want to determine our common ancestor or identify an ancestor who was previously unknown to us. Chromosome browsers help us do that. By determining that an autosomal DNA segment was inherited from a certain ancestor, we can use that segment information in the future to identify matches whose connection to us is unknown. Chromosome browsers also help us triangulate segments of DNA data shared with 2 or more genetic matches. When segment triangulation is achieved, we are able to state with certainty that our triangulated segment was inherited from a common ancestor.
What is a Chromosome Browser?
A chromosome browser is a tool used to visualize the specific portion of a chromosome you share with your genetic match. Chromosome browsers typically display 22 chromosomes as horizontal lines with colored portions highlighting the shared segment between you and your match. Some chromosome browsers include the X chromosome as well. Chromosome browsers give the start and stop points of shared segments, as well as the total length of the segment in centimorgans. Often this data is available in table format below the visual chart.
23andMe, Family Tree DNA, and MyHeritage all provide chromosome browsers. AncestryDNA does not provide a chromosome browser. GEDMatch, a third party DNA analysis tool, also provides several types of chromosome browsers for users who have uploaded their raw DNA results to their site.
Limitations of Chromosome Browsers
Chromosome browsers cannot differentiate between a match on the maternal copy of a chromosome or the paternal copy of a chromosome. Also, the visual appearance of the shared segments are typically not drawn to scale and cannot be relied upon alone. Use the start and stop points and the length of the segment in centimorgans instead.
23andMe Chromosome Browsers
There are two ways to view segment information at 23andMe – on the individual match profile page, and through the DNA comparison tool. To get to the individual match profile page, click on a match, then scroll down to see segment information.
Individual Match Profile Page
To view segment data shared with a DNA match at 23andMe, you must both opt-in to the DNA Relatives feature. To make your genetic information available for genetic relatives to see, choose the “open sharing” privacy setting. Otherwise, matches will have to contact you to make a connection before you can view each others’ segment information. You may have to request that a DNA match share with you before you can view their segment data.
DNA Comparison Tool
Below is the 23andMe DNA Comparison tool, which is a chromosome browser showing several matches being compared to one selected profile. To find the DNA Comparison tool, click on the “Family and Friends” menu item, then click “DNA Comparison.” In the example below, I have selected five genetic relatives (the maximum number) who match my mother, Diana. The names of the matches have been privatized.
This tool shows shared segments of 5 cM and larger (which is smaller than the DNA Relatives threshold, 7 cM). Unlike some other chromosome browsers, you cannot change the threshold of 23andMe’s DNA Comparison tool. The number of lines showing at each chromosome represent the number of profiles you are comparing. Each person’s segments that match Diana are represented by a different color. As you can see, on chromosome 1, two of the segments overlap. This could indicate that the orange and teal matches are related to Diana through a common ancestor. However, it’s also possible that the orange match is on the paternal side and the teal match is on the maternal side. The chromosome browser cannot tell you that information. You must compare the orange and teal matches to each other to determine that they are also related on that segment.
Relatives in Common
One way to compare the data of one of Diana’s matches to the other of Diana’s matches is through the 23andMe Relatives in Common tool. On the match’s profile page, scroll down to see the Relatives in Common list. In the “shared DNA” column, you will see either “yes,” “no,” or “share to see” next to each match.
In the example above, we are viewing the match page of Diana’s genetic match, Cindy. Diana and Cindy have 103 relatives in common. The first relative in common is “Sh.” Diana, Cindy, and “Sh” all share DNA at the same segment, as indicated by the “yes” in the shared DNA column. They are likely all descended from the same common ancestor, and now form a triangulated group.
The third person on the list of relatives in common with Diana and Cindy, “Er,” has a “no” in the shared DNA column. This indicates that Diana, Cindy, and “Er” do not share DNA in the same spot. Diana shares DNA with “Er” at a different place than Cindy shares DNA with “Er.” This could mean that Diana, John, and “Er” inherited different pieces of DNA from the same ancestor, or that Diana is related to Cindy on a different family line than the family line she is related to “Er” on.
Clicking the “no” in the shared DNA column for “Er” takes us to the DNA Comparison Tool. The chromosome browser below shows that Diana, Cindy, and “Er” appear to have an overlapping segment on Chromosome 15.
To confirm that this is not a triangulated segment, we can use the DNA comparison tool to compare Cindy to “Er.” This is a wonderful feature! You choose another person as the main person to compare DNA to. Just click the X next to the person whose test you manage, then add another person who has opted in to DNA Relatives. I chose Cindy. Then I chose “Er” to compare with. Now I am comparing just these two to each other, and not to Diana.
After selecting these two matches, I viewed their segment matching data in the chromosome browser. As you can see below, they do not share a segment on chromosome 15.
Half-identical and Fully-Identical Segments
One more unique thing about the 23andMe chromosome browser is that it differentiates between fully-identical and half-identical segments. This is useful when comparing siblings, as shown in this example from the 23andMe customer care article, “Viewing Shared Segments Of DNA.” Go to the article to see examples of comparing parents to children, grandparents to grandchildren, distantly related individuals, and non-related individuals.
Family Tree DNA Chromosome Browser
The chromosome browser at FTDNA is easy to use. Just view your list of matches in the Family Finder test, select up to seven matches, then click “chromosome browser.” You can change the threshold for matching segments from the default of 5 cM to either 1, 7, or 10 cM. Below you can see the FTDNA chromosome browser. The gray criss-cross sections of the chromosome mean that those are SNP poor areas that did not have enough information to be tested. Most chromosome browsers, including the FTDNA browser, allow you to download your segment data into a .csv file.
The view above is the “chromosome view.” You can toggle back and forth between “chromosome view” and “detailed segment data” which is a table with the segment data including start and stop points of the shard segment.
FTDNA does not allow you to change the main person of the chromosome browser, like 23andMe does, to see if your matches match each other. It also doesn’t show you if any segments triangulate, like the 23andMe shared DNA column in the Relatives in Common list. The FTDNA chromosome browser does include the X chromosome.
MyHeritage Chromosome Browser
MyHeritage is a newer chromosome browser, added in January 2018. Since the March 2018 update, the MyHeritage chromosome browser allows you to compare up to seven DNA matches and also shows triangulated segments. The only thing it doesn’t do is show the X chromosome!
This is the MyHeritage individual match chromosome browser. It is part of the match profile page and it shows how you match to one of your genetic relatives. If you scroll to the “Shared DNA Matches” section of the match profile page, you will be able to see which shared matches have a triangulated segment with you and the match. This is a helpful feature for forming triangulated groups and determining common ancestors!
Hovering over the triangulated segment symbol on the right side of the list tells how many triangulated segments there are between you, the match, and the shared match. Clicking on the triangulated segment symbol brings you to the one-to-many chromosome browser.
The MyHeritage chromosome browser draws a box around the triangulated segment and shades it a bit darker for you to see the segment that triangulates. You can change the threshold for showing triangulated segments to be either 2, 4, 6, or 8 cM.
Below the browser, there is a table entitled “Shared DNA segments info” with all the segment data in table format. You can also download the segment data by clicking “advanced options.” Unlike 23andMe, the MyHeritage chromosome browser does not show fully-identical regions vs. half-identical regions.
GEDMatch Chromosome Browsers
GEDMatch is a third party tool for DNA analysis which has some free tools and some paid tools (called Tier 1). To begin using GEDMatch, you can download your raw data from another website and upload it to GEDMatch as a “kit” to compare with other kits in their database. GEDMatch is useful for comparing DNA tests that were taken at different companies. If you tested at Ancestry but your cousin tested at 23andMe, you can both upload your results to GEDMatch and compare the results there.
One-To-Many DNA Comparison
One of the basic tools at GEDMatch is the one-to-many comparison. This tool compares one kit to all the other kits in the database and gives you a list of all the kits that match. From this list, you can click the “A” to do a one-to-one comparison of two matching kits. If you are using the one-to-many beta tool, as shown below, click on the number in the largest segment column to go to the one-to-one tool.
One-To-One Autosomal DNA Comparison
As you can see in the one-to-one comparison below, there is a blue section on chromosome 1 indicating a significant match region of 64 cM. Yellow indicates a half match, meaning the match occurs only on one of the copies of chromosome 1. You typically only expect to see a full match between siblings.
This one-to-one comparison is the basic chromosome browser at GEDMatch. You can scroll down on the one-to-one match page to see all 22 chromosomes and the x chromosome. To view a one-to-many chromosome browser, you must pay for the Tier 1 tools.
GEDMatch Tier 1 Visualization Options
After you pay $10 for the Tier 1 tools, go to the One-To-Many Comparison tool listed under Tier 1. Then select the kits you would like to compare and click “visualize.” Below is a screenshot of the One-To-Many beta. If you are not using the Tier one link, you won’t be able to check boxes. If you are, then you can check boxes next to the kits you want to visualize in a chromosome browser.
When you click visualize, you’ll see a page to select which type of chromosome browser you want to use. As you can see below, the three chromosome browser options are the 2-D Chromosome Browser, 3-D Chromosome Browser, and Compact Segment Mapper.
2-D Chromosome Browser
Here is an example of the 2-D Chromosome Browser. The colors indicate the size of the shared segment. This helps you disregard small segments. You can pay less attention to blue and pink segments, which are under 10 cM.
For the 2-D Chromosome Browser, you can select up to ten kits to compare. In the example above, you can see that Tom, Dora, and June all share a segment with Diana on chromosome 1. It appears that Tom could overlap with Dora and June, but we need to compare him to them directly to find out. This can be done by doing a one-to-one comparison of Tom with Dora and then Tom with June. Or, you can use the 3-D Chromosome browser.
3-D Chromosome Browser
The screenshot below shows the 3-D Chromosome Browser. It compares each person to each other and indicates a shared segment between 2 kits with a red dot.
The 3-D Chromosome Browser also gives you a matrix/table showing the shared segments between each person being compared. This matrix can save you the time it takes to compare each match with the other matches to see if the segment really triangulates.
Compact Segment Mapper
The third type of one-to-many chromosome browsers at GEDMatch is Kitty Cooper’s compact segment mapper. Hovering over the segment that you want to know more about will bring up a small pop-up with the segment size, start position, and stop position. In this browser, each color represents a different kit/person.
Which Chromosome Browser Should I Use?
If I were to ask a match to transfer to another site in order to use their chromosome browser, I would ask them to transfer to either GEDMatch or MyHeritage. The chromosome browsers at GEDMatch offer the most flexibility. You can compare any kit to any other kit. You can see triangulated segments. However some people may be wary of transferring to GEDMatch due to privacy or concerns about law enforcement accessing their data. The MyHeritage chromosome browser offers triangulation of segments, which FTDNA does not. If 23andMe accepted transfers, I would choose them as well.