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Thread: Is it noise even after phasing ?

  1. #1
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    Is it noise even after phasing ?

    Hello so I made my father do the test and when we phased, 0.2% east asian popped up I thought it was noise but when in the chromosome painter the part where I have east asian become unassigned for him once at 60% confidence (23andme) so I uploaded it onto genesis gedmatch and it appear to be east asian for him too on the 7th and 14th chromosomes (chromosomes painter) here is my kit
    M526312 et here is his TN9946827 (for the info he is 50% polish and the rest is portuguese and french.) Thanks for any kind of help and sorry if my english hurt your eyes .
    Last edited by Luarev; 03-10-2019 at 05:02 PM.

  2. #2
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    Quote Originally Posted by Luarev View Post
    Hello so I made my father do the test and when we phased, 0.2% east asian popped up I thought it was noise but when in the chromosome painter the part where I have east asian become unassigned for him once at 60% confidence (23andme) so I uploaded it onto genesis gedmatch and it appear to be east asian for him too on the 7th and 14th chromosomes (chromosomes painter) here is my kit
    M526312 et here is his TN9946827 (for the info he is 50% polish and the rest is portuguese and french.) Thanks for any kind of help and sorry if my english hurt your eyes .
    Yes, I am 95% sure that is "noise" (defining noise as a more-or-less random error in assignment for small segments). I phased with both of my parents and still have 0.1% "Siberian" (East Asian & NA) on one of my Chromosome 20 pair, the half that I inherited from my mum. She does not have any East Asian & NA, at all (100% European). Of course, it should not be possible for me to get something other than what my parents gave me, so this is "noise."

    On my Chromosome 7 from my dad I have 0.1% NA that he has too there, but even so I treat it still as an error in assignment, because this chromosome 7 from him is an awful messy splash of short, confused segments of different assignments, whereas the rest of his chromosomes are long smooth assignments if correct ancestry (British and Irish, and French).

    I treat anything under 1% as suspicious, especially if it is from the same continent as the rest of your assignments. Different continents (like NA is different from Europe) may in fact show up at the 0.5% level. But anything under that is garbage.
    Paper trail ancestry:
    Mum = 50% Irish, 37.5% Ukrainian, 12.5% Romanian
    Dad = 43.75% French-Canadian, 6.25% Irish, 50% English (25% Essex and 25% Northumberland)
    Big Y 500 = R M269 -> DF27 -> Z195 -> FGC34865 (Western France; ~500 ybp)
    mtDNA = J1c2e
    Most Distant Known Ancestor = Jean Moreau b. 1630s Parthenay, Deux-Sèvres, France
    Surnames = Welch, Chibry, Moreau, Todd, Anderson, Bedford, Joncas, Basaraba

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  5. #4
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    It looks like it may be common northeast European substructure. Unfortunately, there is low overlap between the new 23&me SNPs and the Gedmatch calculators, so the painting isn't as nice for your kits. But, your father has some OK common segments with kit M193492, who seems to be northeast European. The best common areas don't seem to be in your East Asian areas, but this kit has a lot of them. If you chromo-paint kit M193492, you will see what I mean. It wouldn't likely be recent mixing, but something more ancient since it is common for northeast Europeans to have these kinds of segments.

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     Nino90 (03-13-2019)

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    I'd say it's just noise. A lot of people tend to get small percentages from Asia with these calculators. Here's just an example of how phasing affects my results.
    I get 1.20% with Eurogenes K13 admixture with the highest being 6% on chromosome 12 followed by 5.4% on chromosome 7.
    My dad gets 2.28% with his highest at 8.2% on chromosome 7, 6.1% on chromosome 22, 6% on chromosome 14 and then 4.6% on chromosome 12 (my highest).
    My kit that's phased with my dad gets 3.17% Amerindian with the highest on chromosome 10 at 10.1% (higher than both my dad and I and looks like what it would be if I added my dad's Amerindian and my own together). My mum gets 0.72% with her highest being 3.8% on chromosome 7 so maybe that affected the chromosome 10 percentage on the phased kit.
    Ancestry: Ireland (Paper trail ≅ 81.25% Roscommon, 12.5% Galway, 6.25% Mayo)
    Y-DNA (P) ancestor (Y): Kelly b. c1830 in Co. Roscommon (Uí Maine)
    mtDNA (P) ancestor: Fleming b. c1831 in Co. Roscommon
    mtDNA (M) ancestor: McDermott b. c1814 in Co. Roscommon
    mtDNA Great grandfather: Connella b. c1798 in Co. Roscommon (T2a1a8)
    Y-DNA 2x great grandfather: Higgins b. c1816 in Co. Roscommon (R-DF109)
    Y-DNA 3x great grandfather: Fleming b. c1829 in Co. Roscommon (R-Z23534)

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     Ruderico (03-13-2019)

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    Since you don't have any North East European ancestors I would say it is noise.
    Hidden Content

    Eurogenes K13 Mixed Mode Population Sharing:
    1. 63.1% Swedish + 36.9% Spanish_Andalucia @ 2.93

    Dodecad K12b
    7. 66.4% Norwegian + 33.6% TSI30 (Metspalu) @ 3.24
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     Ruderico (03-13-2019)

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    Quote Originally Posted by Nino90 View Post
    Since you don't have any North East European ancestors I would say it is noise.
    His father is 50% Polish and his kit matches many northeast Europeans one on one. My comments were in relation to that kit, which certainly has northeast European ancestry. He has a few remaining inherited areas from his father of this same admixture.

    These kits don't seem to be phased or I would have (and should have noted) that I wouldn't trust admixture tests on phased kits. The Gedmatch phasing is designed to improve the quality of one to one matching and has a warning about using them in admixture tests.

    I don't think the East Asian is noise, but rather ancient substructure. I guess one could call that noise, but it is pretty common and useful for an admixture test to produce these results as long as one doesn't conclude that there is a recent ancestor from China or the far north of Siberia because of it.

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