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  • DWFlineage
    replied
    Originally posted by GregK View Post

    Did you choose "Show All" in the "Derived?" column when searching for the SNPs?

    I know in my case for SNP Y83303 it is one of the SNPs that defines the new terminal block (R-FT89450) that was created from my results and those of one other person, but I don't show it as derived in my results... I believe they need at least ten positive high quality reads to confirm it automatically.

    But it seems on manual review they considered it a match anyway based on these 6 reads.

    y83303.png
    Just tried that, "Show All" in the "Derived" column, no results for either of those two snps that my great-nephew has and I do not. His paternal great-grandfather was my birth father, so there is 3 generations in between us. I have one unnamed snp variant that he does not have. I have ordered the tests at yseq, so we will see. Our autosomal dna results match our relation.

    Best regards, Doug

    Leave a comment:


  • GregK
    replied
    Originally posted by DWFlineage View Post

    I wish I could share a screenshot on here, anyways, BY43076 & BY43077 are snps that Edward has that I do not. The other unnamed non matching snp that Edward has is my only private variant, begins with 238.

    Best regards, Doug
    Did you choose "Show All" in the "Derived?" column when searching for the SNPs?

    I know in my case for SNP Y83303 it is one of the SNPs that defines the new terminal block (R-FT89450) that was created from my results and those of one other person, but I don't show it as derived in my results... I believe they need at least ten positive high quality reads to confirm it automatically.

    But it seems on manual review they considered it a match anyway based on these 6 reads.

    y83303.png
    Attached Files

    Leave a comment:


  • DWFlineage
    replied
    Originally posted by DWFlineage View Post

    I wish I could share a screenshot on here, anyways, BY43076 & BY43077 are snps that Edward has that I do not. The other unnamed non matching snp that Edward has is my only private variant, begins with 238.

    Best regards, Doug
    I ordered BY43076 & BY43077 at yseq so I can confirm whether I have them or not.

    Best regards, Doug

    Leave a comment:


  • DWFlineage
    replied
    Originally posted by GregK View Post

    Have you looked at them in the results browser? Might just not have been enough high quality reads to give a result for those SNPs.
    I wish I could share a screenshot on here, anyways, BY43076 & BY43077 are snps that Edward has that I do not. The other unnamed non matching snp that Edward has is my only private variant, begins with 238.

    Best regards, Doug

    Leave a comment:


  • DWFlineage
    replied
    Originally posted by GregK View Post

    Have you looked at them in the results browser? Might just not have been enough high quality reads to give a result for those SNPs.
    I looked up the two named snps in the 2020 ISOGG and they were named 2018. I will check my results browser. I know that BY snps are only named when two men have them. My great nephew, Edward has not replied to me yet. Of course if he does have a closer Big Y700 match, then I would also match that person about the same as Edward, so I think I am his closest paternal match; as he was raised by non biological father like myself.

    Best regards, Doug

    Leave a comment:


  • GregK
    replied
    Originally posted by DWFlineage View Post
    John,

    Actually, my great nephew, Edward has two not three named snps that I do not have, and I have one unnamed snp that he does not have. I asked Edward to look at his Big Y700 matches; to see if he has any closer matches then me to him; because these two named BY snps must have mutated with his paternal grandfather or birth father, his paternal great-grandfather was my birth father. I could be wrong about these two new BY snps; maybe there is a different explanation for them?

    Best regards, Douglas W. Fisher(Wells)
    Have you looked at them in the results browser? Might just not have been enough high quality reads to give a result for those SNPs.

    Leave a comment:


  • DWFlineage
    replied
    John,

    Actually, my great nephew, Edward has two not three named snps that I do not have, and I have one unnamed snp that he does not have. I asked Edward to look at his Big Y700 matches; to see if he has any closer matches then me to him; because these two named BY snps must have mutated with his paternal grandfather or birth father, his paternal great-grandfather was my birth father. I could be wrong about these two new BY snps; maybe there is a different explanation for them?

    Best regards, Douglas W. Fisher(Wells)

    Leave a comment:


  • DWFlineage
    replied
    Originally posted by JSW View Post
    Yes Doug your family example is closer to the statistics used of dating SNPs

    RE some of the questions earlier
    John, your brother has the same haplogroup designation as you, correct?
    Yes FTDNA gives us the same terminal group. Thus the FTDNA software that does the matching must have ti ability to ignore some number of SNP differences
    I have thought about asking for a second analysis from someone - any recommendations on that thought.?

    Perhaps we are talking about different things? I do not think so These are the same SNPs from the BIG-Y 700 as used by every one else.


    These 10 are your "Private Variants" yes? I do not think that is the case - those are all named SNPs and especially M367 and :L362 have been used for years.

    So my take on it is that my- Y-DNA is a statistically different from what others see
    But that should throw a bit of caution to people trying to us just one set of SNP differences to make a determination of the age of MRCA

    I had 3 SNPs tested at YSEQ in addition to the two above I had CTS6519 tested as a control that I has the right data.
    Here is what YSEQ reported
    ===============
    CTS6519
    [CTS6519]


    hg38 Position: ChrY:14850633..14850633
    Ancestral: T
    Derived: C MY Value C
    Reference: Chris Tyler-Smith (2011)
    ISOGG Haplogroup: R1b1a1a2a1a2a7~
    Comments: Extracted from 1000 genomes data.
    ==================
    M367
    hg38 Position: ChrY:3020587..3020587
    Ancestral: A
    Derived: G MY Value G
    Reference: Cinnioglu et al. 2004
    ISOGG Haplogroup: J (Private)
    Comments: No control in J-P58* but derived in a R-M124* WTY participant
    ==================
    L362
    hg38 Position: ChrY:3020591..3020591
    Ancestral: A
    Derived: T MY Value C
    Reference: Thomas Krahn (FTDNA)
    ISOGG Haplogroup: R2a1a
    Comments: Found in a hg R-L21/P314.2 person
    =========================
    I note for the above I am group R1b and the M367 SNP is usually found in group J and L362 is in R2a
    And my value for L362 of C is not the mutation of A->T that was found before

    So my thought is my results are "unusual"


    RE I suppose I'd assume that not all private variants become haplogroup defining mutation variants?
    I do not think that is the case because while any given SNP mutation is unusual they can and do happen more than once in the history of mankind.
    and my results are an example of that.

    John
    Yes, I agree with your yseq results, Thomas & Astrid Krahn are respected geneticists; and I have had much success testing paternal relatives; in order to confirm timeframes & specific ancestors who carried specific snps. Best regards, Doug

    Leave a comment:


  • JSW
    replied
    Yes Doug your family example is closer to the statistics used of dating SNPs

    RE some of the questions earlier
    John, your brother has the same haplogroup designation as you, correct?
    Yes FTDNA gives us the same terminal group. Thus the FTDNA software that does the matching must have ti ability to ignore some number of SNP differences
    I have thought about asking for a second analysis from someone - any recommendations on that thought.?

    Perhaps we are talking about different things? I do not think so These are the same SNPs from the BIG-Y 700 as used by every one else.


    These 10 are your "Private Variants" yes? I do not think that is the case - those are all named SNPs and especially M367 and :L362 have been used for years.

    So my take on it is that my- Y-DNA is a statistically different from what others see
    But that should throw a bit of caution to people trying to us just one set of SNP differences to make a determination of the age of MRCA

    I had 3 SNPs tested at YSEQ in addition to the two above I had CTS6519 tested as a control that I has the right data.
    Here is what YSEQ reported
    ===============
    CTS6519
    [CTS6519]


    hg38 Position: ChrY:14850633..14850633
    Ancestral: T
    Derived: C MY Value C
    Reference: Chris Tyler-Smith (2011)
    ISOGG Haplogroup: R1b1a1a2a1a2a7~
    Comments: Extracted from 1000 genomes data.
    ==================
    M367
    hg38 Position: ChrY:3020587..3020587
    Ancestral: A
    Derived: G MY Value G
    Reference: Cinnioglu et al. 2004
    ISOGG Haplogroup: J (Private)
    Comments: No control in J-P58* but derived in a R-M124* WTY participant
    ==================
    L362
    hg38 Position: ChrY:3020591..3020591
    Ancestral: A
    Derived: T MY Value C
    Reference: Thomas Krahn (FTDNA)
    ISOGG Haplogroup: R2a1a
    Comments: Found in a hg R-L21/P314.2 person
    =========================
    I note for the above I am group R1b and the M367 SNP is usually found in group J and L362 is in R2a
    And my value for L362 of C is not the mutation of A->T that was found before

    So my thought is my results are "unusual"


    RE I suppose I'd assume that not all private variants become haplogroup defining mutation variants?
    I do not think that is the case because while any given SNP mutation is unusual they can and do happen more than once in the history of mankind.
    and my results are an example of that.

    John

    Leave a comment:


  • DWFlineage
    replied
    Originally posted by John McCoy View Post
    From first (genetic) principles, I see no reason to expect that all SNP's have the same mutation rate, nor even that the actual probability of mutation of a particular SNP will be the same in every individual. The simplifying assumption, that we can obtain reasonable or even realistic results by applying a derived "average" mutation rate, seens to be a good idea, but we still have to validate the results in some way by comparisons with evidence that has verifiable dates. It seems logical to try to make the age estimates as internally consistent as possible, but there is always the possibility that our estimates, or some part of them, are way off! I think it would be an endless task to rework the ages of all nodes of the Y haplotree every time the data change, so it may be that the inconsistencies we see on the current tree are just temporary anomalies waiting to be addressed. A tricky business, that gets more complicated with every Big Y result!
    John, I agree with everything you stated. I know in regard to my own paternal line; in which I have a confirmed paternal line back to an ancestor who was from Romerike, Norway, fought in the Battle of Hastings, 1066, and was awarded land for his service, he was a Knight who lived 1037-1093. I have been able to confirm date timeframes for many of my confirmed snps. My confirmed 13th cousin, confirmed 8th cousin, confirmed 4th cousin, confirmed 3rd cousin 1x removed; all have done snp testing, so this has enabled me to confirm ancestors who actually carried specific snps.

    For instance, my great nephew, whose paternal great-grandfather was my birth father; also did the Big Y 700 testing; and we match all snps except for three unamed snps that I do not have, and I have one snp that he does not have. There are 3 generations between us, so this means a new snp every generation I believe.

    Best regards, Doug

    Leave a comment:


  • John McCoy
    replied
    From first (genetic) principles, I see no reason to expect that all SNP's have the same mutation rate, nor even that the actual probability of mutation of a particular SNP will be the same in every individual. The simplifying assumption, that we can obtain reasonable or even realistic results by applying a derived "average" mutation rate, seens to be a good idea, but we still have to validate the results in some way by comparisons with evidence that has verifiable dates. It seems logical to try to make the age estimates as internally consistent as possible, but there is always the possibility that our estimates, or some part of them, are way off! I think it would be an endless task to rework the ages of all nodes of the Y haplotree every time the data change, so it may be that the inconsistencies we see on the current tree are just temporary anomalies waiting to be addressed. A tricky business, that gets more complicated with every Big Y result!

    Leave a comment:


  • benowicz
    replied
    Thanks to whoever for bringing this thread back to the top of the queue again. It seems like this is going to be a perennial topic.

    I just got BigY700 results for a kit I administer, and although his branch of the phylogenetic tree is not well developed, I did notice that one sub-branch has nearly twice as many SNPs since the MRCA as any of the other six (i.e., average of 35 vs. an average of 18). I have to assume that the six are more indicative of the true TMRCA than the one outlier--although that branch by far has the largest number of participants as well.

    I've searched Google over and over again for the consensus mutation rates, and I keep getting something in the neighborhood of 81 to 85 years, although obviously, as this experience shows, the differences among individual observations can be extreme.

    I've been pouring over the browser details supporting some specific no-calls with my co-administrator, and the possibility has occurred to me that FTDNA has mis-allocated some SNPs that actually belong to the MRCA block within a descendant block. Maybe one or two are mis-allocated, but I highly doubt the whole 17 SNP disparity is mis-allocated.
    Last edited by benowicz; 13 September 2020, 04:47 PM.

    Leave a comment:


  • JD4x4
    replied
    John, your brother has the same haplogroup designation as you, correct? Perhaps we are talking about different things? These 10 SNP differences between you and your brother must not be the same as the "mutation" SNPs that delineate the haplogroups otherwise the two of you would be in 2 different haplogroups. These 10 are your "Private Variants" yes? Granted, I have no understanding of exactly how these are derived, that's just my (tentative) understanding. I suppose I'd assume that not all private variants become haplogroup defining mutation variants?

    For example, looking at R-Y41600 on the Big Y Block Tree, according to the left side (mutation "blocks", afik) I see that there are 3 mutations between R-Y38430 and R-Y41600, which would theoretically mean these two haplogroups would share a CA 450 to 600 years ago or less.

    Leave a comment:


  • JSW
    replied
    Re "t sounds like a CA could be more recent but probably not more distant? " yes i agree at least somewhat.
    To give you one example of how this would be With Big-Y 700 the number of SNPs that differ between me and my brother is ten(10).
    So we are much closer than the calculation will estimate.
    my Confirmed Haplogroup is R-Y41600

    Here is the list of SNPs where we have differences with my brother
    M367, L362, BY23717, BY26105, BY26109, BY26110, BY26111, RS79412108, BY42594, BY227927

    It made me wonder if the test were correct and maybe some were false positives
    As a test of the possibility I paid for Yseq.org to test both M367 and L362 an they confirmed my values were not the expected ones

    John

    Leave a comment:


  • JD4x4
    replied
    Resurrecting an old topic (I'm a relative noob so bear with me).
    So in reading through this I've come to the conclusion that for genealogical research purposes.. if I assume that each branch mutation is (mutation)*200 years (or 150), then the sum of mutations between branches times (200 or 150) gives me a reasonably safe time period to be looking for common ancestors?

    From what I read here (and can comprehend, lol) it sounds like a CA could be more recent but probably not more distant? Thanks for bearing with me and I hope this makes sense!

    Leave a comment:

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