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Thread: Post your PHAX haplotypes here

  1. #1
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    Post your PHAX haplotypes here

    If you have X data you can check out your PHAX haplotypes from the new paper by

    http://www.nature.com/ejhg/journal/v...g2016207a.html

    they are in tables S2-S4 in

    http://www.nature.com/ejhg/journal/v...2016207x10.xls

    I got
    3115=h1,
    5574=h2
    8913=h1.

    From the diagrams it seems that h1 is dominant in all areas except Orkney where h2 draws level. For 5574 h2>h1 in Scotland and Ireland.
    I do have one no read for h1 at rs1441481 (39522460) but I think its fairly clear without that.



    The third, 8913, seems to be wall to wall h1 in Europe so not so useful.
    Last edited by MacUalraig; 01-26-2017 at 09:25 AM.
    WGS (Full Genomes Nov 2015)
    YFull: YF01405 (Y Elite sequencing by Full Genomes Inc. 2013, inc. 435 'reliable' class STRs)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  3. #2
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    Quote Originally Posted by MacUalraig View Post
    If you have X data you can check out your PHAX haplotypes from the new paper by

    http://www.nature.com/ejhg/journal/v...g2016207a.html

    they are in tables S2-S4 in

    http://www.nature.com/ejhg/journal/v...2016207x10.xls

    I got
    3115=h1,
    5574=h2
    8913=h1.

    From the diagrams it seems that h1 is dominant in all areas except Orkney where h2 draws level. For 5574 h2>h1 in Scotland and Ireland.
    I do have one no read for h1 at rs1441481 (39522460) but I think its fairly clear without that.



    The third, 8913, seems to be wall to wall h1 in Europe so not so useful.
    I've checked the one other WGS I have access to from my project and they are
    3115 - h1
    5574 - h1
    8913 - h1

    and have a read for the one position I was missing too. They are same surname as me but don't know their maternal ancestry.
    WGS (Full Genomes Nov 2015)
    YFull: YF01405 (Y Elite sequencing by Full Genomes Inc. 2013, inc. 435 'reliable' class STRs)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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    I am missing something at present.
    Could you please explain where to find this data in either 23&me or ftdna?
    The paper shows that it is not the whole X chromosome but is it just the positions shown in table 1?
    And then what do you do please?
    Out of 64 pre 1800 births 54% Cheshire, 2% Worcestershire, 2% Scottish, 25% south Derbyshire, 6% Burton on Trent area (where 4 counties within 10 miles), 6% Shropshire.One unknown.

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    Interesting study, thanks.

    3115 - h1
    5574 - h1

    For 8913 given the 2 first snp : G at rs12845083 and C at rs12845735 I am either h4, h25 or h28 from the 30 haplotypes in table s4. Too lazy to look to the other snp. Looking at the charts, h4 seems most plausible for me given the high distribution among Hungarians and ancestry on my mother side.

    Judith, using your imputed data from dna land would help.

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  10. #6
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    Quote Originally Posted by Judith View Post
    I am missing something at present.
    Could you please explain where to find this data in either 23&me or ftdna?
    The paper shows that it is not the whole X chromosome but is it just the positions shown in table 1?
    And then what do you do please?
    Judith/Kingjohn,

    As you should see from my sig I did a WGS test at FGC in 2015 and I looked them up in my WGS BAM file. The one I didn't have a WGS read for I double checked in my Ancestry raw file and it was not present. The number of SNPs defining the three haplotypes were defined in the xls sheets I pointed out and number 29,78 and 30 respectively. The extent of their coverage in any chip based test is left as an exercise for the reader ;-)
    WGS (Full Genomes Nov 2015)
    YFull: YF01405 (Y Elite sequencing by Full Genomes Inc. 2013, inc. 435 'reliable' class STRs)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  12. #7
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    Thanks all. Great paper. I look forward to when we can speculate on this forum as to which X haplo types are Steppe, Bell beaker etc.
    Since one of the reference populations was English I would add little by trying (and probably failing, very typo prone) to copy across my positions accurately. If this technique proves valuable then I also look forward to an extraction tool or macro.
    I understand the advice on using my imputed file, but the sheer comparison of the sizes shows how much has had to be inferred. I do love all the fancy scientific words that only mean guessing really.
    Out of 64 pre 1800 births 54% Cheshire, 2% Worcestershire, 2% Scottish, 25% south Derbyshire, 6% Burton on Trent area (where 4 counties within 10 miles), 6% Shropshire.One unknown.

  13. #8
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    England Wales
    Please forgive my naivete but I am new to this 'X searching world'.

    On 23andMe I searched on my mum's raw data, I could only find

    rs12845083 = AA

    Can I deduce anything from it?
    Last edited by Solothurn; 02-13-2017 at 03:16 AM.
    My known ancestral lines:

    U152: A9024/BY3644 @ Vallum Aelium
    H1c3b (mother)
    U4a3 (paternal grandfather's mother)
    U198 (paternal gg grandfather)
    K1a-T195C! (paternal grandmother)

  14. #9
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    Not really, that value appears in 20 different haplotypes on the S4 (8913) sheet.
    WGS (Full Genomes Nov 2015)
    YFull: YF01405 (Y Elite sequencing by Full Genomes Inc. 2013, inc. 435 'reliable' class STRs)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  15. #10
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    England Wales
    OK 'PHAnX'

    Quote Originally Posted by MacUalraig View Post
    Not really, that value appears in 20 different haplotypes on the S4 (8913) sheet.
    My known ancestral lines:

    U152: A9024/BY3644 @ Vallum Aelium
    H1c3b (mother)
    U4a3 (paternal grandfather's mother)
    U198 (paternal gg grandfather)
    K1a-T195C! (paternal grandmother)

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