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  • prairielad
    replied
    Originally posted by John McCoy View Post
    I noticed the problem with female X matches on GEDmatch as well. It goes away if you use a phased kit! I haven't seen any response from GEDmatch on this issue.
    Every chromosome is the same, You are just allowed to filter matches solely on X due to X being an aid at times to determining line of descent due to its unique inheritance pattern.
    If you were allowed to filter matches by chromosome you would see the same thing.
    Each chromosomes comes in pairs(exception for chromosome 23 in males, the pair is made up of an X and a Y)
    Of the pair one is paternal (DNA from father), the other is the maternal(DNA from mother)
    Each position tested has two values, a maternal value and a paternal value, these values can only be one of 4 values (A, C , G or T)
    Matching only requires one of these values to match at each position to create a matching single strand of DNA.
    This will always create false matches (yes, not all small segments are false) as it has your two values to pick from as well as matches two values.

    This is not an issue that can be resolve without phasing (which phases DNA into its single values) unless default thresholds are raised.
    One just has to realize that smaller segments tend to be false due to this, algorithm zig zagging back and forth between maternal and paternal value of each person creating a false segment.
    DNA testing can not say which value at each position belongs to which single chromosome of the pair due to the way it is tested by the companies.

    As mentioned this is not limited to X, if one was able to filter matches per chromosome you would also see this high number of matching (small segments)on each of them as well.

    Males X is "phased" as they only have one, thus only a single value in Raw Data
    A Male to Male compares a single value to single value (less false segments)
    A male to Female compares a singles value to females double values
    A female to female compares each of the double values together looking for only a single value to match.

    Female to Female comparison of X (two values compared to two values) is the same situation that happens on each of the autosomal chromosomes for everyone (male or female) which come in pairs.
    Last edited by prairielad; 23 April 2017, 09:09 PM.

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  • John McCoy
    replied
    I noticed the problem with female X matches on GEDmatch as well. It goes away if you use a phased kit! I haven't seen any response from GEDmatch on this issue.

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  • georgian1950
    replied
    Originally posted by prairielad View Post
    The reason is due to the fact that male to female transmission (father to daughter), there is no recombination. This happens every generation..resulting in the mother passing on sections of her paternal X which skipped a recombination event to all children(most of the time, as recombination does not always happen even when there is another to recombine with).

    Yes male to male X inheritance is wiped out, but the X males receive from mother still follows this pattern.
    The worse case is one line that alternates. Other lines to a lesser extent. It really does not account for the match being way back as some people say.

    On the 'X one-to-many', Gedmatch's default paramenters for minimum segment length is 7 cM. You are working with a X chromosome length of 196 cM if I remember. With normal 50 percent average decay per generation, it would take 5 generations to get down to 7 cM (plus however many you skip, five in the worst case) and that amount of DNA remaining from the common ancestor would unlikely be contiguous. Go down your match's branch and how likely is it that their 7 cM is going to match yours in a 7 cm segment? Yet many females have tens of thousands of matches with the default parameters. I recently saw one with over 25,000. Something else is going on here.

    Jack

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  • prairielad
    replied
    Originally posted by georgian1950 View Post
    People say that, but absolutely no proof of that exists. With two males in a row wiping out the possibility of an X-match, that assertion is absolutely illogical.

    Jack Wyatt
    The reason is due to the fact that male to female transmission (father to daughter), there is no recombination. This happens every generation..resulting in the mother passing on sections of her paternal X which skipped a recombination event to all children(most of the time, as recombination does not always happen even when there is another to recombine with).

    Yes male to male X inheritance is wiped out, but the X males receive from mother still follows this pattern.

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  • georgian1950
    replied
    Originally posted by KATM View Post
    I have read that segments on the X chromosome can go further back in time than segments on the autosomal chromosomes 1-22.
    People say that, but absolutely no proof of that exists. With two males in a row wiping out the possibility of an X-match, that assertion is absolutely illogical.

    Jack Wyatt

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  • KATM
    replied
    I suppose you have already plotted out the ancestors who could have contributed to your X inheritance, using charts such as those found at Blaine Bettinger's blog, or these pedigree style charts.

    I have read that segments on the X chromosome can go further back in time than segments on the autosomal chromosomes 1-22. If that is the case, perhaps there is a relative who could have contributed these X segments, but has not yet been found in your research.

    If you have researched far back on yours and these two matches' trees, and are sure there is no way you can be related on the X chromosome, is it possible that you are more distantly related to either of these matches via a common population?

    I grant you that the 7.65 cM segment match to your male 2nd cousin once removed may be harder to explain, if his X-contributing ancestors don't match yours.

    What is the longest block for your female 5th cousin? Does she match you on any autosomes, as well? In this article "X Chromosome Recombination's Impact on DNA Genealogy," there is this statement in the "Tips and Warnings About Using X-DNA" section:
    Because X-comparison tools compare both X chromosomes when comparing women, do not set a too low SNP matching threshold. It's possible that it could suggest half matches where it is merely chance that the numerous SNPs match. In other words, comparisons with and between men are typically more reliable.

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  • SueA
    started a topic False positives

    False positives

    I'd be interested to know what the theories are, if any, about false positive X-matches.

    I ask because Family Finder says I have X-matches with two people, one male and one female, who I know are related to me but in such a way that we can't share any X-DNA.

    The chromosome browser gives these figures:
    (male, my 2nd cousin once removed) 1 block of 7.65 cM
    (female, my 5th cousin) 7 blocks totalling 19.89 cM

    So where do these 'X-matches that aren't real' come from?
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