Understanding x-match

[alice]

I am baffled by the match described below. Please, can someone with a better understanding of the x-chromosome help me?

F and M are the father and mother, respectively, of Daughter 1 (D1) and Daughter 2 (D2).

F and his children have a fairly strong autosomal match (38 cM in one segment) with Cousin (C).

M and C have no autosomal or x match.

F and C have no x match.

From triangulation it is clear that the match between F and C is on F's father's side, not his mother's.

Yet, D1 and D2 both show x matches of the same 7.9 cM segment with C. How is this possible, since the x that F passed on to his children was from his mother?

Thanks a lot.

[prairielad]

Depending on size of X match, ignore it as it maybe false.
It is recommended that only X matches over 10cM will be valid.

FTDNA declares anyone a X match if segment is 1cM/500SNPs or greater.

Women to women X comparisons will have more false X matches(they each have two X values) then a male to male comparison (they only have one X value each). Algorithm is only selecting 1 value to match in a single sequence of values to create a matching segment.

[prairielad]

Phasing parents to child at Gedmatch may show that X match is not valid if this match also utilizes Gedmatch.

[alice]

X-comparison on Gedmatch

I tried comparing daughters' phased paternal kits with C's kit but got an error message: "both kits must have an x-chromosome." I don't understand because of course both do have an x-chromosome.

[ltd-jean-pull]

If C is not an X-match to F nor M, but F&M's daughters are an X-match then is very likely to be due to them being "identical by chance" on the X-chromosome.

There is a very good description of Identical By Chance in this article by Roberta Estes.

https://dna-explained.com/2016/03/10/concepts-identical-bydescent-state-population-and-chance/

If you have a look at a male kit and a female kit on Gedmatch the females have several-fold more X-matches than the males. Because they have two X-chromosomes and males have one you'd expect them to have only twice as many X-matches as a male, so many of these X-matches can't be real.

[prairielad]

I tried comparing daughters' phased paternal kits with C's kit but got an error message: "both kits must have an x-chromosome." I don't understand because of course both do have an x-chromosome.

How long ago were these kits uploaded to Gedmatch, Original FTDNA uploads required one to upload 2 files, autosomal Raw Data and X Raw Data. X Raw Data was optional.
Now one has to upload the concatenated Raw Data file from FTDNA which has X included.

Run Gedmatch diagnostic utility on kit numbers in question and see if X (chromosome 23) shows a Number of SNPs used.

[dna]

If C is not an X-match to F nor M, but F&M's daughters are an X-match then is very likely to be due to them being "identical by chance" on the X-chromosome.

There is a very good description of Identical By Chance in this article by Roberta Estes.

https://dna-explained.com/2016/03/10/concepts-identical-bydescent-state-population-and-chance/

If you have a look at a male kit and a female kit on Gedmatch the females have several-fold more X-matches than the males. Because they have two X-chromosomes and males have one you'd expect them to have only twice as many X-matches as a male, so many of these X-matches can't be real.

Yes, Identical By Chance.

Yes, females have two X chromosomes.

However, you also need to take into account that females are related to more people in their family, than males are. Please take a look the following two pictures that show how very different X chromosome inheritance patterns for females and males are:





The above images came from the page http://www.genie1.com.au/blog/63-x-dna


Mr. W

[alice]

X-match and phasing

Thanks to everyone who replied to my question; you have been very helpful. My latest steps may be helpful to others as well.

FTDNA shows no X-match between F and C, but both daughters show X-matches with C. (X-match of 3 cM on FTDNA and 7 on Gedmatch).

On Gedmatch I checked using the diagnostic utility and it showed F's X-chromosome having only about 10,000 SNPs. I deleted that kit and re-uploaded the raw data file and F's X-chromosome went up to 19,000 SNPs.

I then re-ran the daughters' phased files and compared the phased X-chromosomes with C's. No match. However, their unphased files do show the 7 cM match (though there is no X-match with M, their mother).

So my conclusion is that this is all much ado about nothing and I am confirmed in my original assessment of where the connection between F and C lies. I wish there were a way for FTDNA to do some of this legwork for us and not show the match in the first place!

[snetphilie]

One thing nobody ever seems to mention is the fact that part of the X chromosome recombines with the Y Chromosome.

So it is in fact possible for you to inherit part of your X chromosome from your mother's father's father. Your mother's father's X partially recombined with his Y, so one of your mother's X's contains a portion of her father's Y, and then her two X's recombine and you likely get some of that passed onto you.

The same holds true for your father. Part of his X and Y recombined, so if you are male, you received part of the X he got from his mother in your Y chromosome, and of course the rest of the Y from him, but even his Y was a combination of his father's X and Y. If you are female, you still receive part of the Y that your father got from his father.

Moral of the story is, the X match doesn't filter out the part of the X that recombines with the Y, so it is not a very accurate indicator of anything.

Oh, and here's a video that shows how the X/Y recombination is different than the other chromosomes! https://www.biointeractive.org/class...n-y-chromosome