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X-DNA Advanced Advanced topics about X-Chromosome matching and anthropologic blocks based on SNPs and/or STRs.

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  #1  
Old 29th October 2017, 03:03 PM
alice alice is offline
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Understanding x-match

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.
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  #2  
Old 29th October 2017, 04:27 PM
prairielad prairielad is offline
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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.

Last edited by prairielad; 29th October 2017 at 04:32 PM.
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  #3  
Old 29th October 2017, 04:33 PM
prairielad prairielad is offline
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Phasing parents to child at Gedmatch may show that X match is not valid if this match also utilizes Gedmatch.
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  #4  
Old 31st October 2017, 10:19 PM
alice alice is offline
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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.
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  #5  
Old 31st October 2017, 11:03 PM
ltd-jean-pull ltd-jean-pull is offline
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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...on-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.

Last edited by ltd-jean-pull; 31st October 2017 at 11:05 PM.
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  #6  
Old 1st November 2017, 01:31 AM
prairielad prairielad is offline
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Quote:
Originally Posted by alice View Post
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.

Last edited by prairielad; 1st November 2017 at 01:33 AM.
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  #7  
Old 1st November 2017, 03:02 AM
dna dna is offline
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Quote:
Originally Posted by ltd-jean-pull View Post
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...on-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
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  #8  
Old 2nd November 2017, 11:31 AM
alice alice is offline
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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!

Last edited by alice; 2nd November 2017 at 11:35 AM.
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