X-Chromosome Matching at Family Tree DNA

Just as they promised, and right on schedule, Family Tree DNA today announced X chromosome matching.  They have fully integrated X matching into their autosomal Family Finder product matching.  This will be rolling live today.  Happy New Year from Family Tree DNA!!!

In the article, X Marks the Spot, I showed the unique inheritance properties of the X chromosome.  In a nutshell, men only inherit one copy from their mother, because they inherit a Y from their father, but women get a copy from both parents.  Still, you don’t inherit parts of your X from all of your ancestors, so knowing your own X inheritance pattern can help immensely to rule out common genealogy lines when you match someone on the X.

In their informational rollout, Family Tree DNA provided the following information about their new features.

Here is the menu link to the Family Finder Matches menu.

x match 1

On the Family Finder Matches page, there is a filter to show only X-Matches.

x match 2

When you use the X-Match filter on a male Family Finder kit, you should get only matches from the maternal X-Chromosome.

x match 3

Next, like other Family Finder Matches you can expand the advanced bar for a match and click to add the match to the Compare in Chromosome Browser list.

x match 4

Matches are added to the Compare in Chromosome Browser list. You could go right to the Chromosome Browser by clicking on the compare arrow at this point.

x match 5

Next we can also go right to the Chromosome Browser.

x match 6

The Chromosome Browser also lets you filter the match list by X-Matches.

x match 7

Here are three immediate relatives. The first two share X-Chromosome DNA. The third (green) one does not.

x match 8

When we scroll down to the X at the bottom, we see that X-Matching is displayed for the first two but not the third.

x match 9

Moving to the Advance Matching page, X-Chromosome matches have also been integrated.

x match 10

X-Match is an option that can be checked alongside other types of testing.

x match 11

198 thoughts on “X-Chromosome Matching at Family Tree DNA

  1. Hi Roberta,
    I am adopted and am very new to DNA. I had both my MtDNA and Family finder test done at Family Tree DNA as well as Ancestry and 23&Me. With FTDNA, I have many x-matches, but only two men. One is a 4th-remote cousin and the other is a 5th-remote cousin. After reading your information about the x-chromosome, I understand that the only way that these two men can be related to me is through my mother’s line. What is my next step? Do I concentrate on their common matches with me (though neither of them share matches with each other), or should I look at their shared matches with me and only concentrate on x-matches from that point?

    I started looking at both men on the chromosome browser and noticed that they match in the same place on the x-chromosome as well as 3, 6, 11, & 12. I started comparing chromosomes of other x-matches and found that many matched on the same segment of the X and 11 chromosomes, though they only show up at the 1cm range. I am not sure what to do with this information though it seems as though I might have found something important.

    Should I keep working to identify everyone that match in the same segment of the X and 11 chromosomes and then compare them with some tool like dnagedcom or something? Should focus only on people with the longest block (over 20 to my match max of 53); or highest shared Cm (over 50 to my match max of 70); or only my x-matches with the longest block or the highest shared Cm?

    I started looking at my 2nd-4th cousins and looking at matches I had in common and writing down all my x-matches from there, but I understand that this won’t tell me whether the match is on my mother or father’s side. I had 1 person (5th-Remote cousin on family finder) who matched from my MtDNA and looking at the matches we have in common, there are 2 X-matches (neither of them are the 2 male X-matches). Then when I click on those X-matches, I get more. I’m lost. Do I just keep adding the X-matches of my X-matches?

    I can see how the X-matches will be very important for me, but I don’t know what they actually mean for me since the two male X-matches and my one MtDna match are so distant. Is it worth pursuing or should I go back to my 2nd-4th cousin matches or keep looking at chromosomes (especially #11 where so many are stacked)?

    Sorry for this really long question but i am SO confused!! I hope you can give me some advice and/or point me in the right direction … or give me some links so I can learn more.


    • I generally work the X chromosome last. FTDNA only lists your X matches who also match you on another chromosome. I start with what I do know and with my largest matches and go from there. You need to join the adoption DNA group. Look under the help tab at the top of my blog page. They have a process for you to work through that you will find very helpful. Best of luck to you in your search.

      • Thanks! I was getting overwhelmed at the extra information from the Chromosome x and trying to figure out what that data meant. I did think that I could narrow down my search to just my maternal line from it and then go back to largest matches. However, I will do what you said. I appreciate the help!!

  2. I only have one X match out of 400+ matches. That sounds low or is that normal? And it would be on my mothers side correct? All of her roots are in the south which puzzles me as most of my mtDNA is Native America or French Canadian with a small portion of Ulster Irish into Pennsylvania.

    Another question: I’m looking to find a unknown maternal grandfather for my daughter. Some of her matches I know are on her maternal grandmothers side, She has one close match where that person matches on a number of chromosomes plus the X. I have no clue who she is because she didn’t put any identifying information on the site. I have a birth certificate and oral history that don’t match. I need to e-mail her I guess but I have to wordsmith it carefully as I don’t want to upset someones DNA tree with something that has been hidden in the closet for years. Anything I should be looking for in the DNA?

    Thanks for any help.

    • Hi Roger. You only get X matches if you also match that person on other segments as well. That is why the number of X matches are so low.

      Yes, it would be on your mother’s side. Good luck on your second quandary. I would tread lightly and see if you can establish contact first.

      • This is a big problem that I encountered on the site. the x matching is very ineffective on FTDNA as far as I can see – it leaves out a lot of matches – I have one match over 20 cms only on the x on GEDMATCH and over 100 matches, while familytree has about 3 matches. – as far as familytree is concerned the match is not there????
        Why is that?

      • Family Tree DNA only shows X matches if there are other matches as well over the match threshold. X matching alone, especially without other matches, can be deceptively high and from very far back in time, which does not really play by the same rules as the rest of the autosomes. I’m assuming that is why.

      • So…my Dad matches me. This means that somehow he and my mother match on her maternal line?

      • Sorry, on further reading, I see that I get the X from both parents, so of course he should show up.

  3. My wife wants to find her roots in England and Russia or perhaps Germany through her fathers family lineage (x chromosome testing) We live in North America and she was born in Poland. Her father died when she was very young and had no contact from that side of the family. She really wants to know where her paternal grandmother came from. How accurate will the results be using the x chromosome test?

    • The X chromosome will not be of any special us for this. The rest of the autosomal DNA will be of more use. Finding her father’s lineage will be the easiest if she has someone, like her mother or a sibling of her mother to test, so she can tell who is from her mother’s side. Any of her father’s relatives would be good to test too.

  4. Roberta, quick question (sorry if it is stupid, I’m new to all of this). As a female, do my x-matches match up with both sides, since I receive x from both parents, or would my results be indicative of my mother’s side only? I’m completely confused. I’ve got 12 pages of x-matches on FTDNA. THANKS!

  5. How useful are the cM lengths on the X chrome in trying to narrow relationship range?

    I’m trying to figure out a family mystery surrounding an Italian great-grandfather. Both my father (Chas) and his first cousin (Endicott) have a common female match (Ann) who is estimated 2nd-3rd cousin. Endicott and Ann match on two places on the X for at 45.5 cM and 29 cM. for a total of 74.5 cM. Endicott’s mother and Chas’ father are siblings. Hence that’s why Endicott has an X match with Ann and not Chas. Can I use the 74.5 cM X match to solidify the estimated 2 – 3rd cousin match estimate? Other data for the matches:

    Endicott to Ann – 218 cM Autosomal on 21 segments with largest 4 at 38cM (6204SNP), 36 cM (10,300 SNP), 27cM (5649 SNP) and 19 cM (4400 SNP). Of the 21 segments, 7 are under 5 cM.

    Chas to Ann – 240 cM Autosomal on 17 segments with largest 4 at 50cM (8153 SNP), 33 cM (4566 SNP), 32 cM (6786 SNP), and 25 cM (4729 SNP.) Of the 17 segments, 6 are under 5 cM.

    My limited knowledge tells me that Chas/Endicott must be 2nd cousins to Ann with very little chance that it’s an outlier to 2nd cousin 1X removed. Thank you so much for any insight you may have.

    • I would rely on other information from other chromosomes primarily. I have found the transmission characteristics of the X to be somewhat different than the rest of the chromosomes so I could be hesitant to apply the same guidelines to the X as to the other autosomes. I don’t believe Blaine Bettinger included the X in his cM study, but it would be very interesting if he were to do so.

  6. Okay so two questions.
    1. I have one of my parents and my kit on here. My dad. If I run in common matches only that are x-match, would those all be relatives from his mothers side?

    2. If I run to exclude all common matches with him, woudl those x-matches all be from my mothers side?

    I think x-match is pretty darn cool. It makes the autosomal have some teeth. How did they do it though after all the hee haw about how they leave off that?? Why are they unable to get the haplotype from the same test?


  7. Pingback: DNAeXplain Archives – Introductory DNA | DNAeXplained – Genetic Genealogy

  8. Hi,

    Would you be able to tell me what the significance of each chromosome strand? I am just getting started and just want to know when there are matches on particular chromosomes if that has any particular meaning.

    Thank you

  9. Okay. I’ve read through the responses, and I want to see if I have this right. My father-in-laws father was adopted. He has had his DNA done through ancestry, and I’ve uploaded it to FTDNA and he has plans to pay the transfer fee. He gets very few X matches in GEDMATCH, but assuming I understand this- the X matches he gets are from his Mom…. (not adopted). Those pages and pages of non-x matched people on Gedmatch are from his Dad (adopted)?

    • Partly right. You KNOW that the X matches are from him Mom’s side. The non-X matches may be from his Dad’s side or people from his Mom’s side that don’t match on the X, but do match on other chromosomes. So you can’t say any more about the non-X matches than that.

  10. On gedmatch I have a 50 cm match on the X chromosome (1 segment only) but there is no autosomal match at all. Is this a false positive sort of a thing? A coincidence or are they actually related but so far back only an X segment shows up?

  11. Hi,

    FTDNA shows that my father has 8 people with whom he X-matches. However, when I look up some of those 8 people in the Chromosome browser, not all of them illustrate matches on the X in the browser itself. Why is that?

    Some do of course, but others don’t and I find that puzzling — is it because the X-matches in those cases do exist but are so small that they simply don’t appear on the X browser image?

    Many thanks.

    • Sorry to disagree with Roberta, but I don’t think is necessarily a bug. I think your first instinct was correct. What did you have the cM threshold set to (drop down in top left column)?

      Sometimes if you have the cM threshold set to 5+ cM (the default), certain matching DNA segments do not appear in the chromosome browser because the segments are smaller than 5+ cM. This includes the X-chromosome segments. However, if you lower the threshold to 3+ cM or 1+cM, the hidden segments will appear.

      If I am not mistaken, I believe that 3+cM is still an acceptable threshold for a match by relation, whereas 1+ cM could also be a match by chance.

  12. Hello,
    I have an x match on chromosome. This person also matches me on two other places. What does this mean?

  13. For a female if she has a male match that does not show as an x match in Ftdna, but the match is shown as being in the 3rd to 5th range, does that mean they are not related or that this male did not contribute to x.

  14. I personally think that the X-matches are from the mother’s side not the direct personal mother, any mother of any of your fathers or fathers fathers. I have an X-match with a segment of 22 for a person whom I know is related to me from My fathers grandmother’s Side. if it doesn’t complicate things. to make it simple, as I understand it. It is not direct to any X holder.

  15. Looking at my results on FTdna, I see an X match with a relative from my father’s side and no X match with a relative from my mother’s side. Is this normal?

    • Females can have X matches yo both. Makes only have X matches to their mother’s side. If a male has an X match to their father’s line, it’s either IBC or through a different maternal line he is unaware of.

  16. Roberta,

    As you know, FTDNA has since sorted our match lists by father’s side and mother’s side. since I don’t have my father’s DNA, I asked them to sort my list by father’s side by comparing the DNA of my matches to the DNA of my father’s paternal first cousin Evelyn — whose mother was the sister of my Dad’s father Thomas Powell Jr. As you also know, in doing this, my matches that are now identified (in blue) as being on my father’s side are those on my father’s “paternal” side ONLY, not his maternal side.

    Some of my matches identified as being matches on my father’s “paternal” side (i.e., who match my father’s paternal first cousin Evelyn) are also showing as an X-chromosome match.

    Since these are DNA-proven matches on my father’s father’s side of the family, does their matching me on the X-chromosome mean they match me through their mother’s side of the family?

      • So my paternal x chromosome matches who are females could have inherited the matching x chromosome from either their mother or their father, whereas my paternal x chromosome matches who are male could only have inherited the matching x chromosome from their mother. This would indicate that my paternal x chromosome matches who are male are related to me and my father on their mother’s side, correct?

  17. I forgot to mention in the first paragraph that I also had my mother’s DNA to compare my matches to when sorting my match list by mother’s side and father’s side.

  18. We had both of my husband’s parents do the family finder test and were shocked to see they matched each other at the 2nd to 4th cousin range AND are an x-match! Does this mean that they are related through his dad’s mother’s line? It might be a bit of a family scandal because his dad’s mother has never approved of his mom!

  19. I have a X-match with another female, what does that mean?
    We have a Chromosome match on 2, 14 and 22 – what does these mean?
    Why is there a difference on cM, ftDNA show a 84 cM and GEDmatch a 54cM?

  20. I have a question. My Paternal Uncle matches me on 1 and a third segments of my X chromosome. My father is deceased so I can’t have him checked. Can an Uncle have the same x chromosome passed down to him that my father gave to me?

    • Your father’s brother and your father could have the same X chromosome. They could only inherit an X from their mother. So yes. The X your match your uncle on is from his and your father’s mother.

  21. On my FF results most of the “X match” are not on the X chromosome on the Chromosome Browser. Do they have another way of determing maternal linkage or is this a mistake? Thanks

  22. Sorry, I don’t quite understand. Does the term “X match” mean that shared genetic material is on the X chromosome? If so, most of the X matches given in my “matches” are not on the X chromosome, even if I change the filter from 5 cM to 10 cM.

    • It means that in ADDITION to another chromosome match, you also match on the X. Also, lowering the threshold means changing it from 5 to 1, not 5 to 10 – that’s raising the threshold.

  23. Yes Thank you. That seems to be the answer; lowering the threshold to 1 cM breaks up the chromosome matches and shows some fragments on the X chromosome.

  24. Can you draw any general conclusions from the visual pattern of the chromosome browser? That is for example, if the filter is set low to <1 cM, and among the larger 50-70 cM fragments, the pattern shows many small colorations on many chromosomes, versus a single long match on one chromosome? Is that how the allogrithm for degrees of kinship works?

  25. Thank you very much. This citation has a lot of valuable information about the total shared DNA and degree of kinship. I am still curious about the the visual pattern of the shared DNA distribution on the chromosomes. I am guessing having the total DNA in a single block on one chromosome rather than broken up into small segments on many chromosomes, probably indicates more recent kinship.

  26. Hi Roberta,
    My half sister (we have same mother) does not match me on our x chromosome. Is it safe to say that any x matches I have would be from my paternal side?
    Thank you for that you do!

    • No, you got one X from your mother and one from your father. The X you got from your mother is the one from her “other” parent. In other words, your sister received one of your mother’s X chromosomes intact, and you received the other.

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