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Big Y - beyond the terminal snp?

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  • Big Y - beyond the terminal snp?

    so..... 11 very long months (yes, eleven, i do not want to talk about it) after ordering my father's Big-Y, the results finally came in today.
    R-YP450 (green) was given as the terminal snp, there are however a few more downstream (blue). does that mean he was not tested for those?


    YDNA_R-YP450.jpg

  • #2
    I am just learning myself, but I think those are your private variants. Those are the SNPs found for him which no one else has. If another person tests and has one of those, then a new terminal SNP will be defined for your father and that person.

    Big Y may cost a lot, but it is a test which keeps on giving (in many cases).
    Last edited by georgian1950; 31 March 2020, 02:56 PM. Reason: spelling

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    • #3
      Originally posted by georgian1950 View Post
      I am just learning myself, but I think those are your private variants. Those are the SNPs found for him which no one else has. If another person tests and has one of those, then a new terminal SNP will be defined for your father and that person.
      i think i understand what you are saying...? or not. (this is very new to me, sorry.) however, if i understand correctly, the blue are named subs and then there are as yet unnamed private variants within those? the info given in the block chart states that there are 1 to 2 participants for each of the blue subs, so they have been tested for those however they did not apply to my father... i am very confused.

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      • #4
        Originally posted by Kohlehydrat View Post

        i think i understand what you are saying...? or not. (this is very new to me, sorry.) however, if i understand correctly, the blue are named subs and then there are as yet unnamed private variants within those? the info given in the block chart states that there are 1 to 2 participants for each of the blue subs, so they have been tested for those however they did not apply to my father... i am very confused.
        I haven't been able to locate the display that you show so that I can view it with my data. How did you find the display?

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        • #5
          Originally posted by georgian1950 View Post

          I haven't been able to locate the display that you show so that I can view it with my data. How did you find the display?
          thank you for taking the time to look! that is the more compact haplotree and snps view that you can find under y-dna. below, i am posting the big-y blocktree view for R-YP450 (i covered the country flag circles in gray for privacy).
          edit: wait... are you saying you cannot see the images i uploaded here?

          YDNA_R-YP450-blocktree-view2.jpg
          Last edited by Kohlehydrat; 1 April 2020, 07:38 AM.

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          • #6
            Thanks. I am a bit confused myself. I think FTDNA may still be comparing your private variants and if it finds someone else who has one of the same, it will create a new terminal SNP for you. That is what happened with me. Apparently you are in the group on the right, or it would have given you a SNP further down.

            I would be patient for a few more days. I hope someone who knows more about this than me will chime in.

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            • #7
              ah good to hear it went further for you - did you have matches?
              yes, my father is in the group to the right, on the left are the subs. as one can see, this branch is not exactly very populated so i am not holding my breath for any developments soon.

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              • #8
                I had one kit I managed which had been upgraded to Big Y-500 in mid-2018, and was given a new terminal SNP. In December 2019, without any further testing, I noticed the terminal SNP had changed. As with georgian1950, it appears that someone matched one of the private variants for this kit at that time, almost 18 months later. Since then, that kit was upgraded to Big Y-700, with results in Feb. 2020, and the waiting game begins anew.

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                • #9
                  i see, thank you for the info, KATM. my father is 90, i do not think there will be any upgrades for him in the future should ftdna come out with a new big-y (and i think they have gone through all 4 of his samples, i was too tired to ask them after all the hassles). if he gets a new terminal snp without testing, great, but otherwise this will be the end of the road.

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                  • #10
                    Originally posted by Kohlehydrat View Post
                    ah good to hear it went further for you - did you have matches?
                    yes, my father is in the group to the right, on the left are the subs. as one can see, this branch is not exactly very populated so i am not holding my breath for any developments soon.
                    Well, I had the one match who formed the new terminal SNP with me. Our Big Y results came through at the same time. At first FTDNA gave us the same existing terminal SNP, but a few days later it updated us with a new terminal SNP based on us each sharing a private variant. I believe that is not done automatically, but has to be examined by a researcher, so maybe you will have a surprise real soon.

                    Interestingly, I was not a Y-111 match with the guy I formed the new SNP with.

                    Now the question is how far back our common ancestor is? I think many interpret Big Y results to put the common ancestor too far back. One co-administrator of a subclade project that I am in thinks the CA is 500-1000 years back, but an autosomal comparison suggests that my second great grandfather was responsible for a NPE. The original FF does not compare well with the new AncestryDNA test, so it looks like I will have to break down and order an AncestryDNA test for a better (and more convincing) comparison.

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                    • #11
                      With Big Y, they tested your father for all the regions of the Y chromosome that they test for, I think the coverage is 75% of the chromosome. So with that it should have covered testing if he belonged to one of those downstream terminal SNPs and he was found to be negative for those. You can search his results for the named variants that are listed downstream to see what his results were for them to be sure. Type in the part after the dash (FGC22480) and change the drop down in Derived? to Show All. Then you can see his result vs the standard reference at that position. If you click on the FGC22480 link, it will bring up the results for that area of the test and show you what the readings were.

                      So it looks like at the moment your father doesn't match anyone with an SNP that is any more recent than R-YP450. As georgian1950 and KATM have stated there are comparisons done manually for new variant matches. They do it manually in order to try to make sure that the variant is a location that can be used for branching and not one that may happen at random across the population.

                      Looking at yfull, it looks like the estimated date for R-YP450 is between 50 AD and 900 AD. All the people who have sent their results to yfull that are Y chromosome descendants from R-YP450 come from the same region of the world. Between Sochi and Chechnya is the rough range of the people listed there, which is a distance of only around 500 km. So it looks like that helps pin you to a fairly recent time which is getting close to being when records may have survived and a relatively small region of the world. So if you weren't sure where your father's paternal line came from, it looks like you may have gotten a fairly good hint of where they were 1000 years ago and can study the history of the area and the people to learn more.

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                      • #12
                        Originally posted by bhemph View Post
                        With Big Y, they tested your father for all the regions of the Y chromosome that they test for, I think the coverage is 75% of the chromosome. So with that it should have covered testing if he belonged to one of those downstream terminal SNPs and he was found to be negative for those. You can search his results for the named variants that are listed downstream to see what his results were for them to be sure. Type in the part after the dash (FGC22480) and change the drop down in Derived? to Show All. Then you can see his result vs the standard reference at that position. If you click on the FGC22480 link, it will bring up the results for that area of the test and show you what the readings were.

                        So it looks like at the moment your father doesn't match anyone with an SNP that is any more recent than R-YP450. As georgian1950 and KATM have stated there are comparisons done manually for new variant matches. They do it manually in order to try to make sure that the variant is a location that can be used for branching and not one that may happen at random across the population.
                        Pretty much this, I will add that the OP linked to the SNP Browser which is not fully connected into the BigY testing results. Only positive results from the BigY get included in the SNP Browser.

                        Chances are you can goto your BigY "Results" section, set the "Derived?" column to "Show All" then search for those individual named SNP's from the SNP Browser and have it return "No" in the "Derived?" Column.

                        I imagine part of why they don't include negative results from BigY in the SNP browser is for performance reasons. But of course, there also is the chance that you actually had a "no call" event happen on a given marker, in which case the result in the "Derived?" column would be a "?" instead.

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                        • #13
                          As suggested by Georgian1950 and bhemp, your father's SNP might be updated any day from a closer match sharing a SNP downstream, which has happened to me about six times after more men tested, and most recently after I convinced a cousin to expand 111 STR to Y700, while I have never upgraded from Y500.

                          YFull might branch the result differently if it is transferred there. It is a waiting game to see if anyone else posts SNP results at FTDNA or YFull. Many of the same admins at the FTDNA haplo projects are also using YFull, which is no big secret.

                          Unlike the report by Georgian1950 for his SNP branch, the two results for "my" branch on the FTDNA Public Haplotree (I-A11036 as of today) is a member of my Y-STR subgroup defining a probable common ancestor from mainly STR testing, Whereas, YFull assigns the two of us to a branch I-A11035 (as of today) that they estimate to within average 350 YBP, which happens to align splendidly with genealogical record trace to TMRCA to an unknown father of three possible brothers in the year 1771.. We were formerly assigned upstream SNPs by FTDNA that sometimes matched YFull's branches, but sometimes not, and using STRs only were both matching other men at estimated 3000 YBP for TMRCA..

                          You give yourself the best chance of your father's terminal moving downstream by using both databases, FTDNA and YFull, and contacting admins or matches who might help. One of my most helpful contacts possibly shared a male ancestor at estimated 1900 YBP, not genealogically traceable, but we have enjoyed a helpful correspondence. I would not have come into any contact with him if I had been at only one Y database. I will add that similar to GEDMatch, this allowed my results to compare to results tested with WGS services and men from all over the world.As stated above, a decent .BAM file is a gift that can keep on giving!
                          Last edited by clintonslayton76; 27 April 2020, 05:14 PM.

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                          • #14
                            I have a similar issue with the BLUE or Downstream reporting. For the part of the Haplotree where BY3354>BY4016>BY4015, I have several men who tested positive for BY3354, but show BY4016 as Blue. I have one who tested positive for BY4016, and three who tested positive for BY4015 and ASSUMED Positive for BY4016.

                            How can BY3354 be determined as the terminal SNP unless BY4016 is tested as negative? How can the Haplotree be verified as BY3354>BY4016>BY4015 unless some is positive for both BY4016 and BY4015? Without testing the BY4016, why couldn’t BY4015 and BY4016 be branches off of BY3354?

                            i have asked FTDNA support these question, but have received no satisfactory answer. Their reply is that the tree is correct.

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