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Evaluating a Big Y match

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  • 1798
    replied
    Originally posted by Brunetmj View Post
    I did a search on this topic but they ended up being subclade specific. Is there a quick way , that is a general way, to evaluate a Big Y match ? For example the highest novel variant matches I have are 54. However it is shown this novel variant match happened a few thousand years old. How many novel variants would a person share if the match was 500 years ago?
    Could someone summarize a quick and dirty evaluation method.?
    I am particularly interested in more recent times (last 600 hundred years). What would their novel variant sharing look like? What should I look for?
    These are very wise words from a poster about NGS testing.
    "The reality of NGS testing is, if you don't have any close STR matches, then you're unlikely to have any close Big Y matches. Because of this, many Big Y testers end up as singleton branches within a high level "paragroup", having a long list of private SNPs that no one else have. Genealogically relevant information will be gained from NGS testing ONLY if you have matches of interest within a relevant time frame. Whether this is the case can be assessed pretty reliably by looking at your STR matches. Unless there is some unclear phylogeny within your matches due to ambiguous STR signatures, and revealing the exact structure of that phylogeny is critical to understanding the history of your ancestry then discovering your own branch's SNPs amounts to an expensive novelty item."

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  • 1798
    replied
    Originally posted by JohnG View Post
    In my surname project three of us took the Big Y. Two are 5th cousins with a common ancestor born about 200 years before we were born. The other is our 11th cousin with a common ancestor born about 1550, not quite 500 years ago. I match the 5th cousin on 106 novel variants. I match the 11th cousin on 101. I am digging into the results and by looking at my data I find a few errors in these and will have and adjusted number and tree of what our common ancestor likely had and what each of us has lots and gained since then. We have a SNP that now has a name, BY653, shared with two others who took the Big Y and do not have our surname or geographic origin. There are a couple other as yet unnamed SNPs that seem to relate to just this group of 5 people. The two more distant relations match me at 57 and 58 novel variants. I think this will also be adjusted after I do some work with understanding my results. I think the difference between 101 shared variants and 58 shared variants is a couple thousand years!
    If five variants are equal to 500 years then 106 must be equal to at least 10,000 years. So that would put P312 back in the Mesolithic.

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  • 1798
    replied
    Originally posted by JohnG View Post
    No, of those 106, 42 are shared only with folks I relate to by surname in the last 500 years. 1 is By653 with a total of 5 people, and below DF27. The other 63 I have not exactly tabulated but some are under DF27 and most of the others under P312 but not DF27.
    So they are under P312! The average number of Big Y SNPs under U106 is 36.

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  • JohnG
    replied
    Originally posted by 1798 View Post
    Have you got 106 SNPs downstream of DF27 from your Big Y test?
    No, of those 106, 42 are shared only with folks I relate to by surname in the last 500 years. 1 is By653 with a total of 5 people, and below DF27. The other 63 I have not exactly tabulated but some are under DF27 and most of the others under P312 but not DF27.

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  • 1798
    replied
    Originally posted by JohnG View Post
    In my surname project three of us took the Big Y. Two are 5th cousins with a common ancestor born about 200 years before we were born. The other is our 11th cousin with a common ancestor born about 1550, not quite 500 years ago. I match the 5th cousin on 106 novel variants. I match the 11th cousin on 101. I am digging into the results and by looking at my data I find a few errors in these and will have and adjusted number and tree of what our common ancestor likely had and what each of us has lots and gained since then. We have a SNP that now has a name, BY653, shared with two others who took the Big Y and do not have our surname or geographic origin. There are a couple other as yet unnamed SNPs that seem to relate to just this group of 5 people. The two more distant relations match me at 57 and 58 novel variants. I think this will also be adjusted after I do some work with understanding my results. I think the difference between 101 shared variants and 58 shared variants is a couple thousand years!
    Have you got 106 SNPs downstream of DF27 from your Big Y test?

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  • lgmayka
    replied
    Originally posted by JohnG View Post
    I think the difference between 101 shared variants and 58 shared variants is a couple thousand years!
    YFull says that R-BY653 began to split up about 4500 years ago.

    But analysis of the newest entry is not yet complete.

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  • JohnG
    replied
    Originally posted by Brunetmj View Post
    In several of the 54 to 52 novel variant matches it does not list a difference in the differences column. So your suggestion is a good one, but for me not quick. Well maybe just answer this question, how much novel variant exists is say someone who shared a common ancestor but in the last 500 years? I guess to narrow down my question is there a relationship between the novel variants shared and the closeness in time to the person who shares them ? What is the average novel variants shared by family members?
    In my surname project three of us took the Big Y. Two are 5th cousins with a common ancestor born about 200 years before we were born. The other is our 11th cousin with a common ancestor born about 1550, not quite 500 years ago. I match the 5th cousin on 106 novel variants. I match the 11th cousin on 101. I am digging into the results and by looking at my data I find a few errors in these and will have and adjusted number and tree of what our common ancestor likely had and what each of us has lots and gained since then. We have a SNP that now has a name, BY653, shared with two others who took the Big Y and do not have our surname or geographic origin. There are a couple other as yet unnamed SNPs that seem to relate to just this group of 5 people. The two more distant relations match me at 57 and 58 novel variants. I think this will also be adjusted after I do some work with understanding my results. I think the difference between 101 shared variants and 58 shared variants is a couple thousand years!

    Leave a comment:


  • Brunetmj
    replied
    Would this be a fair summary of this post?

    1. Know the definition of a novel variant- i.e.a SNP that is newly discovered -not necessarily unique to your family line

    2. Know your subclade since you need to differentiate SNP's found in your novel variants from those found in other groups

    3. If you want to assess if a person is in your family line "in recent times" they must also posses the SNP's found in your particular sub branch of a subclade. Example: My main subclade is FGC5494. To be a recent family member(last 500 years or so) the person in question would have to be S2202.
    Point 3 reinforces point 2 in that you need to know your subclade and branches.
    Last edited by Brunetmj; 19 July 2015, 10:42 AM.

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  • 1798
    replied
    Originally posted by Parameswara View Post
    You can not compare autosomal test (Microarray Chip) with Big Y (Next Generation Sequence). Autosomal test chip only read those 700,000 SNPs. Big Y read about 11-12 millions base-pair in your Y. So basically it's a lot more than 700,000. Of course you get (comparing to the reference sample) very few mutation in interpretation result. So the result is just small number SNPs. You will get those 11-12 millions in Y-BAM files.
    Thanks, I didn't know but I do now. I think that 300$ would be enough for the Big Y test.

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  • Parameswara
    replied
    Originally posted by 1798 View Post
    If the price of the Big Y does not come down then those that did the test already will remain in limbo. The FF test with 700,000 SNPs is only 99$ and the Big Y for a small number of novel variants is 575$. If there were health related SNPs in the Y chromosome the price would be 99$ also.
    You can not compare autosomal test (Microarray Chip) with Big Y (Next Generation Sequence). Autosomal test chip only read those 700,000 SNPs. Big Y read about 11-12 millions base-pair in your Y. So basically it's a lot more than 700,000. Of course you get (comparing to the reference sample) very few mutation in interpretation result. So the result is just small number SNPs. You will get those 11-12 millions in Y-BAM files.

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  • 1798
    replied
    If the price of the Big Y does not come down then those that did the test already will remain in limbo. The FF test with 700,000 SNPs is only 99$ and the Big Y for a small number of novel variants is 575$. If there were health related SNPs in the Y chromosome the price would be 99$ also.

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  • lgmayka
    replied
    Originally posted by MMaddi View Post
    Does YFull even make an official estimate for CTS2509, based on analysis of BAM files from CTS2509+ men, or are you just extrapolating, based on your SNP counting?
    YFull's TMRCA for R-Z325 (which it considers to be on the same level as CTS2509) is 2600 ybp.

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  • 1798
    replied
    Originally posted by MMaddi View Post
    Iain McDonald, whom you cite approvingly all the time, disagrees. Based on comparison of a dozen or more Big Y results from CTS2509+ men, he estimates CTS2509 is about 2,100 years. I would take Iain's estimate over YFull's estimate, since Iain has access to a larger dataset for CTS2509. Does YFull even make an official estimate for CTS2509, based on analysis of BAM files from CTS2509+ men, or are you just extrapolating, based on your SNP counting?

    Plus, you can't seem to decide whether you prefer a SNP mutation rate of 150 or 136 years. You don't seem to want to even consider FGC's 90 rate of 90 years, which I pointed out is based on significantly larger coverage of the y chromosome. If you pick and choose your SNP mutation rate to come up with the answer you want to get, that's not very scientific.
    I didn't write the script for Yfull. R-Z325CTS2509/S1734 * Z324 * FGC362/Y1407/Z8172... 3 SNPsformed 3300 ybp, TMRCA 2600 ybp

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  • MMaddi
    replied
    Originally posted by 1798 View Post
    Yfull gives a TMRCA of 4,800 for Z9 and your SNP is 12 downstream of Z9. At 150 years per SNP that would put your CTS2509 at 3000 ybp and you and your match are one below it.
    Iain McDonald, whom you cite approvingly all the time, disagrees. Based on comparison of a dozen or more Big Y results from CTS2509+ men, he estimates CTS2509 is about 2,100 years. I would take Iain's estimate over YFull's estimate, since Iain has access to a larger dataset for CTS2509. Does YFull even make an official estimate for CTS2509, based on analysis of BAM files from CTS2509+ men, or are you just extrapolating, based on your SNP counting?

    Plus, you can't seem to decide whether you prefer a SNP mutation rate of 150 or 136 years. You don't seem to want to even consider FGC's 90 rate of 90 years, which I pointed out is based on significantly larger coverage of the y chromosome. If you pick and choose your SNP mutation rate to come up with the answer you want to get, that's not very scientific.

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  • 1798
    replied
    Originally posted by MMaddi View Post
    Well, that's wonderful, but what does it have to do with you disagreeing with my estimate that my 83/111 match who shares one of my Big Y singletons with me has a TMRCA with me of 1,500 years or maybe less? You could have left it at just saying that you may not be right. The rest has nothing to do with the question we're discussing.
    Yfull gives a TMRCA of 4,800 for Z9 and your SNP is 12 downstream of Z9. At 150 years per SNP that would put your CTS2509 at 3000 ybp and you and your match are one below it.
    Last edited by 1798; 16 July 2015, 12:47 PM.

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