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  • X Chromosome match observations

    Whee! The new X chromosome browser is going to be fun to investigate.

    I was surprised by the high percentage of my total matches that show up using the X filter -- eight pages out of 51 total. I randomly picked four to start with, and they all appear just to the right of the centromere (the narrow waist) at 53 to 67 Mb. The segment size is ~ 3 cM.

    I suspect there may be something odd about this segment, as other people have not reported so many matches.

  • #2
    I'm getting a lot of matches in that section of the X-chromosome too.

    Here's my blog post about my matches:

    http://cruwys.blogspot.co.uk/2014/01...-matching.html

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    • #3
      I have 17 pages of X matches out of a total of 75 pages of matches at FTDNA.

      Comment


      • #4
        I have 7 pages of X matches out of 26 using the X filter. Segments are all over on both arms. This is one time I wish we could match more than 5 matches in the Chromosome Browser.

        Originally posted by Ann Turner View Post
        Whee! The new X chromosome browser is going to be fun to investigate.

        I was surprised by the high percentage of my total matches that show up using the X filter -- eight pages out of 51 total. I randomly picked four to start with, and they all appear just to the right of the centromere (the narrow waist) at 53 to 67 Mb. The segment size is ~ 3 cM.

        I suspect there may be something odd about this segment, as other people have not reported so many matches.

        Comment


        • #5
          Originally posted by Ann Turner View Post
          Whee! The new X chromosome browser is going to be fun to investigate.

          I was surprised by the high percentage of my total matches that show up using the X filter -- eight pages out of 51 total. I randomly picked four to start with, and they all appear just to the right of the centromere (the narrow waist) at 53 to 67 Mb. The segment size is ~ 3 cM.

          I suspect there may be something odd about this segment, as other people have not reported so many matches.
          Ann
          I have 68 matches and my son has 7.. You helped me with his X matches some years ago at 23andme .. so I am pretty clear.. but his largest match, which is still small, I do not share. It is I think 7.9cM..

          I do not remember any discussion about "Compound Segments"? What exactly does that mean? I am seeing it discussed elsewhere tonight..

          Thanks much..

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          • #6
            My mother has 10 X matches. There are 2 X matches on my mother's in common list. I have no X matches other than my mother.

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            • #7
              Originally posted by Jackd View Post
              My mother has 10 X matches. There are 2 X matches on my mother's in common list. I have no X matches other than my mother.
              I think this is the explanation for my son " segments align purely by chance" ~ thanks Debbie Kennett
              Last edited by Kathleen Carrow; 2nd January 2014, 07:03 PM.

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              • #8
                X good and bad

                Today's X match does have a "feature" we need to be aware of. It works just like the rest of the FF test (the autosomal) in that if a match includes a segment from either side, paternal or maternal, it reports it. Even if the matching segments are from both sides.

                Why is this something to be aware of? Because for a male looking to assign his matches to his maternal side, a small X match may be misleading.

                As has always been the case, Family Finder will consider any kit a match that meets certain criteria, one being a longest block match over 5.5cM, with additional criteria added, this means the smallest longest block match will end up being near 7.7cM.

                Since the X match must first meet autosomal matching criteria, any X match will (just like the autosomal 3rd segments and beyond) be anything from 500 SNPs and above, meaning 1.x cM segments will be reported. There are many cases where small segments match to one side, and other small segments match to the other side. Most of the time these are called population segments because they indicate some previous endogamy or smaller population pool the SNPs flowed from.

                I have a distant cousin match of 25cM in FF. My son does too, however, now with X matching, my son also has a 1.97cM match to my cousin (his paternal) on the X. I don't. We can't check his mother's kit because X is only reported if the autosomal matches over 7.7cM (effective) first. In gedmatch she does show the X match, as does my son. The answer is simple, my cousin has an even more distant match on the X to my wife, carried over to my son. Of course all of it may be IBS as well but that depends on where the line is drawn on IBS for a male's X doesn't it. Would I personally look into a maternal X 1.97cM match for my son? Nope! Not when he has a paternal 25cM match as well.

                If he did not have my test, or my wife's test compare to, he might assign this match as a maternal side match - based on the X match. The X match is maternal, true, the closest relative and the one FF is basing the match with to begin with, is on my side, paternal.

                Use caution with following any small segment match in a SNP test, including an X match. The 1/2 IBD matching system will find a match regardless of which line it comes from. The FF test will report any and all 500SNP matches from either lineage, once the autosomal criteria is met.

                Now that's not really bad news; it is a caution. The good news is that we now have the X included in the FF test. Like all parts of the test, using the proper techniques and criteria, we can use it to our advantage.

                Good luck to all!

                Matt.
                Last edited by mkdexter; 2nd January 2014, 07:28 PM.

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                • #9
                  Hi Matt thanks for the explanation. Just wondering if it is possible that one of my X matches who I share just about 3.43 with could be real? They do match my Mom at 23andme but not on the X. The reason I wonder is because I share more here with this match before the X matching than my Mom did. I also noticed that this match also shares small cm of 2-3 with over 700 SNPs in spots with another match that I have on chromosomes 4,5,15, and then on the X. This other match and I share several spots on the X. The original match that I'm talking about has Colonial ancestry. I'm not sure about the second one, but looks Colonial as well. Hopefully I wasn't too confusing explaining my question.

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                  • #10
                    Originally posted by Táltos View Post
                    Hi Matt thanks for the explanation. Just wondering if it is possible that one of my X matches who I share just about 3.43 with could be real?
                    Hi,

                    The best answer here is a definite maybe. :-/ It is hard to say more unless we can phase your X-Chromosomes.

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                    • #11
                      Originally posted by Rebekah Canada View Post
                      Hi,

                      The best answer here is a definite maybe. :-/ It is hard to say more unless we can phase your X-Chromosomes.
                      Thanks Rebekah. By phasing the X chromosomes you mean between my Mom and myself? And if so, this feature would it be available from FTDNA soon?

                      Comment


                      • #12
                        Why do they use such tiny segments for X chromosome matching?

                        My mother's brother's son matches her on the X chromosome! He got his X from the Cappelle sul Tavo, Italy side of the family. I can tell that on Gedmatch. My mother has no Italian ancestors.

                        My mother got her X chromosomes from the German and French branches of the family. A few of her 6 pages of X chromosome matches show some German ancestry, but most are colonial American and UK.

                        When did we get the Matrix feature? I never noticed it before. It looks like it's going to be much more useful than the X chromosome.

                        Comment


                        • #13
                          23andme vs FTDNA X-match

                          Comparing two brothers:

                          23andme (1 segment)
                          X chromosome, 26.1 cm, 2047 SNPs

                          FTDNA (2 X segments)
                          X chromosome, 3.99 cm, 650 SNPs
                          X chromosome, 8.51 cM, 750 SNPs

                          Does anyone else have this much of a discrepancy?

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                          • #14
                            Originally posted by MoberlyDrake View Post
                            Why do they use such tiny segments for X chromosome matching?
                            The whole test uses tiny segments. Any two kits just need to match in one place by 5.5cM, then by a portion of that, then by a sum over ~20cM and then the rest of the segments can by anything 500 SNPs and above, anywhere, including the X.


                            Originally posted by MoberlyDrake View Post
                            When did we get the Matrix feature? I never noticed it before. It looks like it's going to be much more useful than the X chromosome.
                            http://forums.familytreedna.com/show...04&postcount=1

                            Comment


                            • #15
                              Originally posted by ajmr1a1 View Post
                              Comparing two brothers:

                              23andme (1 segment)
                              X chromosome, 26.1 cm, 2047 SNPs

                              FTDNA (2 X segments)
                              X chromosome, 3.99 cm, 650 SNPs
                              X chromosome, 8.51 cM, 750 SNPs

                              Does anyone else have this much of a discrepancy?
                              Please post the start and stop locations on both tests.

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