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  • #31
    Big Y's usefulness

    I was denied service by a Y genomic processor and took Big Y as a second choice, and my primary reason to do so was to get a BAM file that could be interpreted by a service that would explain the assignation of a terminal SNP. The cost of these tests implies that some accountability is in order.

    FTDNA does not provide that feedback. One service assigns me a SNP that is recognized on ISOGG while FTDNA assigns what looks to me like a novel variant, although this is on the cusp of my understanding about SNP analysis. Even the merest theoretical YBP that I get from another service has some obvious thinking behind it, but the new "tree" used by FTDNA has disconnected me from the previous I-Y3153 terminal I1a2a1a1a1b5 as ISOGG shows it, so I have no idea if FTDNA has me upstream or downstream from my previous terminal they assigned.

    I am essentially given an either/or situation by two services: either I am part of a downstream branch I1a2a1a1a1b3 +A1890, +A1892, +A7425 as recognized by ISOGG and YFull, or I am something FTDNA has conjured up that is not recognized or explained, I-F1997. Who has it right, or at least will explain the basis? FTDNA certainly does not.

    As a One Name Study admin, it is hard for me to recommend the cost of any Y genomic sequencing without the ability to generate a BAM file or get any answer other than the 8-ball "Ask again later" that I got from FTDNA. It makes me wonder about the person behind the curtain. If I am truly "out standing in my field" as a bran-new example of something, okay, but the issue is not so much ZERO matches as a constantly shifting now-you-see-them-now-you-don't terminal SNP assignment.
    Last edited by clintonslayton76; 5th February 2018, 07:26 PM. Reason: Redundant

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    • #32
      Originally posted by clintonslayton76 View Post
      I was denied service by a Y genomic processor and took Big Y as a second choice, and my primary reason to do so was to get a BAM file that could be interpreted by a service that would explain the assignation of a terminal SNP. The cost of these tests implies that some accountability is in order.

      FTDNA does not provide that feedback. One service assigns me a SNP that is recognized on ISOGG while FTDNA assigns what looks to me like a novel variant, although this is on the cusp of my understanding about SNP analysis. Even the merest theoretical YBP that I get from another service has some obvious thinking behind it, but the new "tree" used by FTDNA has disconnected me from the previous I-Y3153 terminal I1a2a1a1a1b5 as ISOGG shows it, so I have no idea if FTDNA has me upstream or downstream from my previous terminal they assigned.

      I am essentially given an either/or situation by two services: either I am part of a downstream branch I1a2a1a1a1b3 +A1890, +A1892, +A7425 as recognized by ISOGG and YFull, or I am something FTDNA has conjured up that is not recognized or explained, I-F1997. Who has it right, or at least will explain the basis? FTDNA certainly does not.

      As a One Name Study admin, it is hard for me to recommend the cost of any Y genomic sequencing without the ability to generate a BAM file or get any answer other than the 8-ball "Ask again later" that I got from FTDNA. It makes me wonder about the person behind the curtain. If I am truly "out standing in my field" as a bran-new example of something, okay, but the issue is not so much ZERO matches as a constantly shifting now-you-see-them-now-you-don't terminal SNP assignment.
      Are you a member of the I-Z140 Project? If so I would ask one of the administrators about your terminal SNP relative to your ISOGG/YFull designation. They may be able to shed some light on I-F1997.

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      • #33
        Thanks for suggestion

        >>Z140 Haplo Project

        Yes, I did almost immediately, and my admin stated that FTDNA appears to be using a novel variant and not a terminal, that is the basis of my posting:

        "F1997 is not on the Z140 Project or YFull Tree. I have repeatedly advised members to ignore the FTDNA advice to test it​. So far, it has proved to be a Private Novel Variant for a SLAYTON family member."

        That family member would be me.
        Last edited by clintonslayton76; 7th February 2018, 01:18 PM. Reason: more info

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        • #34
          Originally posted by clintonslayton76 View Post
          >>Z140 Haplo Project

          Yes, I did almost immediately, and my admin stated that FTDNA appears to be using a novel variant and not a terminal, that is the basis of my posting:

          "F1997 is not on the Z140 Project or YFull Tree. I have repeatedly advised members to ignore the FTDNA advice to test it​. So far, it has proved to be a Private Novel Variant for a SLAYTON family member."

          That family member would be me.
          I think it is safe to say your haplogroup is the one recognized by ISOGG and YFull, only you have a private SNP found in your family line.

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          • #35
            Originally posted by clintonslayton76 View Post
            I am essentially given an either/or situation by two services: either I am part of a downstream branch I1a2a1a1a1b3 +A1890, +A1892, +A7425 as recognized by ISOGG and YFull, or I am something FTDNA has conjured up that is not recognized or explained, I-F1997. Who has it right, or at least will explain the basis? FTDNA certainly does not.
            It is not an either/or case. Different places will have different data and ways of designating a haplogroup. I looked up F1997 over at Ybrowse. Appears to have been a singleton found on a person from a different major haplogroup. FTDNA system must have given you that haplogroup because it is a named variant. You or your haplogroup admin could try contacting FTDNA staff to fix that if no one who is A1890+ or whatever upstream haplogroup you are from has F1997.

            Originally posted by clintonslayton76 View Post
            As a One Name Study admin, it is hard for me to recommend the cost of any Y genomic sequencing without the ability to generate a BAM file or get any answer other than the 8-ball "Ask again later" that I got from FTDNA. It makes me wonder about the person behind the curtain. If I am truly "out standing in my field" as a bran-new example of something, okay, but the issue is not so much ZERO matches as a constantly shifting now-you-see-them-now-you-don't terminal SNP assignment.
            As more data comes in, it is normal for the terminal SNP to change. Specially when more people take the test and share variants with the test taker. An uncle's kit that I manage has changed haplogroup designation twice since the initial Big Y results came and gave him a downstream haplogroup from his predicted one. A few of his matches were given the wrong haplogroup (entirely different major haplogroup) after the first update to their shared haplogroup. I had to report that and FTDNA fixed it. BAM files will come in time. The few Big Y tests (from STR matches) I was waiting for have arrived. It is just a matter of time.

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            • #36
              Thank you Contemplator, but the issues are: 1) why am I not notified of a changed terminal SNP and 2) why is the I-F1997 assignment never explained by FTDNA when requested. The folks at YSeq and YFull at least try to explain, whereas FTDNA generated a canned statement that essentially says we do not have to to explain this.

              I am trying to educate myself through communications with haplo admins and these Help Forums, but it seems that the service I use for most of my testing does not intend to help. You have given me more information about this than the people who got my money or use my results for their calculations, and that does not seem right to me.

              You or your haplogroup admin could try contacting FTDNA staff to fix that if no one who is A1890+ or whatever upstream haplogroup you are from has F1997.
              My Haplo admin (only one responds) prefers low resolution 12 or 25 Y-STR followed by SNP testing, which is logical for their purpose, but not very helpful to a surname project where most men assume that the highest resolution Y-STR (67-111) is the best bang for the buck, as well as the most interpretable by a non-scientist. For that reason, that admin puts little weight on the SNP assigned by FTDNA, and I have no hope of resolution from the tactic you suggest.
              I used to have upstream Big Y matches, but not any more.
              Last edited by clintonslayton76; 11th February 2018, 01:06 PM.

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              • #37
                Contemplator....

                Much respect for Thomas Krahn for creating this and to you for being able to use it, but...
                I looked up F1997 over at Ybrowse. Appears to have been a singleton found on a person from a different major haplogroup.
                is a statement I cannot test, because I have never figured out how to find a SNP at YBrowse. I have stared at that site for years without cracking the code of knowing how to find a SNP. I do not expect a lesson here, merely that I have tried and it is not explicit to me.

                YFull (I am on the "I" tree there as Yf06160) shows F1997 at ChY (hg19) 15813372 and ChrY position (Hg38) 13701492 as one of my five private SNPs. That is all that I have gleaned so far. The man there stops me at A7435,1890,A1892 on his tree, but shows F1997 as a 4 star out of 5 Positive, while A1892 is 5 star. I see no "age" data for F1997, while the A1892 shows his estimate of 2800 YBP.

                Clearly I am a singularity at FTDNA for this private SNP, but at least a match for one at YFull as well as by my Haplo admin by virtue of A1892 etc.
                Last edited by clintonslayton76; 11th February 2018, 04:32 PM. Reason: spacing

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                • #38
                  Ideally, yeah it would be great if FTDNA could tell us more about our results. Maybe at some point that was more easy for them to do. Many of the SNPs being found are new and all data is dependent on the few that have it. We know how people can copy trees and that could affect what conclusions we form with so little data.

                  I think this is why FTDNA caters to admins. Without interested researchers all this data will mean a whole lot less to all of us and FTDNA simply can't keep up. Maybe as time goes on, they will be better equipped to answer questions such as yours. After all, the customer reps aren't going to have a whole lot to offer in specifics that require someone from the lab to answer.

                  YFull will show that SNP as private because it bases its tree only on data uploaded to their system. Their age estimations require at least two kits and are not displayed on the tree until the next tree update. YFull will also have less data than FTDNA given that not everyone uploads to YFull. Some as you may know don't bother with YFull, because of free analysis from other places or project admins. No one would be against the idea of FTDNA having more answers, but maybe that isn't feasible at their prices? I don't know.

                  Originally posted by clintonslayton76 View Post
                  I have stared at that site for years without cracking the code of knowing how to find a SNP. I do not expect a lesson here, merely that I have tried and it is not explicit to me.
                  Well too bad I've giving you one! To search for a named SNP like F1997, you simply search for that name. In the "Landmark or Region" text field, type that name or that of any SNP. Hit search. Then at the bottom in the SNP section you will see a bar with the name of the SNP you searched for. Click it and you will see the position of that SNP as well as perhaps a comment. When a SNP is added, a comment is usually made about what haplogroup it comes from. If you see it is from a haplogroup that is different well then you know it could be a parallel mutation or some unreliable one. The year it was added to the system is also noted in this case 2011.

                  If you want to search for a position for example 13701492 then you type "chrY:13701492..13701492". Obviously it could be a range if you want to see more than just one point in the chromosome. In which case those two numbers will be different, to form a range. Not all named variants will be on the system right away. So any newly named BY or BZ SNPs by FTDNA may take a while to get into that system. You can however look up their positions to see what is the expected reference.

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                  • #39
                    In the "Landmark or Region" text field, type that name or that of any SNP. Hit search. Then at the bottom in the SNP section you will see a bar with the name of the SNP you searched for.
                    I have done both of these things in the past and I appreciate your explanation, but I see no explicit SNP section on the page, the DETAILS item shows SNPS which does nothing for me when I click it. Obviously this is not my forte since your explanation seems logical but I do not see anything other than the region as a red line on a scale. I will keep at it, because what is accessible to you is surely accessible to me.

                    It has been a no-go for me to get my members to consider Big Y, then upload a RAW file somewhere else for $50. This is too technical for them, and they would resent the expense, even when we have offered General Funds to help, because we mostly wanted to confirm the suspicion that we were not all genetically related by a surname variant. I might be "out standing in my field" with F1997 until after I am gone. I would be happy if one of my cousins got cooperation from the Y genome service that arbitrarily denied service to me (I asked for an approximate date of completion and had my credit charge reversed as a result!), but that was much more expensive than Big Y.

                    I am aware that YFull has a limited database, but I have received NEWS items and updates as e-mails from YFull, but absolutely nothing from FTDNA. The explanation of why a SNP is seen as private at one site and not used as a terminal, but used as such at another site, is problematic for me, seems arbitrary. But again, thanks for taking the time.
                    Last edited by clintonslayton76; 11th February 2018, 05:43 PM. Reason: clarity

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                    • #40
                      Originally posted by clintonslayton76 View Post
                      ...the DETAILS item shows SNPS which does nothing for me when I click it.
                      Maybe it is a web browser issue? In the details section, there are subsections. One of them is "SNPs". In it, there is a long rectangle (red outline) that is highlighted (yellow) with the name of the SNP above it. If you move the mouse over it, it will give you the SNP's position. If you click it, it loads a page with a few details (if any). It isn't a whole lot but sometimes that is all one needs.

                      Originally posted by clintonslayton76 View Post
                      It has been a no-go for me to get my members to consider Big Y, then upload a RAW file somewhere else for $50. This is too technical for them...
                      I know how that goes. I've been surprised that I managed to convince any of my project members to bother taking the Big Y. In this specific surname project there had been no Big Y tested members until I talked a few into doing it. Then a few more did it later. While I have told them about YFull, I have never pushed for it because I too worry it would be too technical for them. Free analysis elsewhere with my explanations have managed to be enough so far.

                      Originally posted by clintonslayton76 View Post
                      ...but I have received NEWS items and updates as e-mails from YFull, but absolutely nothing from FTDNA. The explanation of why a SNP is seen as private at one site and not used as a terminal, but used as such at another site, is problematic for me, seems arbitrary. But again, thanks for taking the time.
                      To be fair, YFull only has one service. They analyze the raw data of NGS type tests like Big Y. FTDNA has a larger scope, so they may not handle the details as well. They do seem to get better little by little over time at least.

                      As for choosing SNPs being arbitrary, well it sort of is true. Each place has their standards and amount of time allotted to doing so. This is also true with 3rd party analysis. If you are project admin, then you may have better luck with getting the customer reps for group projects to yield better answers than regular customer reps. In the contact form, choose the Group Project category, choose the dropbox item indicating you are a project admin, and use your GAP login as your kit number. It may help to imagine all these different haplogroup designations as drafts. Some drafts from some places will be more accurate than others. In time they change.

                      I just think it is simply an error in the FTDNA system based on what you have said. While 3rd party analysis will likely have an actual person be more involved in the haplogroup designation I would think due to less responsibilities.

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                      • #41
                        Thanks again, Contemplator

                        If you are project admin, then you may have better luck with getting the customer reps for group projects to yield better answers than regular customer reps. In the contact form, choose the Group Project category, choose the dropbox item indicating you are a project admin, and use your GAP login as your kit number.
                        I have always followed that procedure, but have not got any explanatory response.

                        As to a browser issue on Ybrowse, I often open OE 11 and Chrome in order to have two FTDNA sessions open, and I have not checked the Details for SNPs with OE ever, only Chrome, where hovering the mouse over SNPS does nothing for me. I will try this with OE soon. I passed on MS Edge.

                        Thanks so much for your help, and if we seem to have strayed from the root issue, a reminder to any readers is that my FTDNA Big Y hg38 took away all matches that used to show in Big Y,but that still show grouped in my Haplo Projects (I1a, I+Z140, etc) as part of the same ancient lineage. In other words, FTDNA is a minority view for my terminal SNP when all other interpreters show me as part of a +Z2538 and +A1892 lineage,and FTDNA used to have me connected to +Y3153 with some matches. Now all gone on FTDNA.

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                        • #42
                          Contemplator, Ybrowse responds!

                          I looked up F1997 over at Ybrowse. Appears to have been a singleton found on a person from a different major haplogroup.
                          This responded today, and I do not know what "hg O3" person means, but it is gratifying to see the same info as you.

                          I am none the wiser about research, if any, on this SNP, esp as to why Ybrowse did not respond yesterday, but I have had some strange interactions between Win 10 Fall Creators and Google Chrome.

                          Perhaps the terminal SNP of F1997 will trigger more research, so let's keep a good thought.

                          Thanks!
                          Last edited by clintonslayton76; 12th February 2018, 05:29 PM. Reason: correction

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                          • #43
                            Originally posted by clintonslayton76 View Post
                            This responded today, and I do not know what "hg O3" person means...
                            In this case "hg" is haplogroup. As for O3, that would be a specific haplogroup. As you may see over at ISOGG, they still use the old style of haplogroup naming. If you go to ISOGG and click on YSNP Tree, you can look for O3. In the current (2018) version, there is no O3. But as you might recall, the Ybrowse details indicate that SNP was added in 2011. So if you look at the 2011 version of ISOGG's tree, you can find a O3 or what would be named with the SNP naming scheme as O-M122. Now if you search for M122 in the 2018 version of the tree we can see it is now O2. As you can see the SNP naming scheme is more consistent.

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                            • #44
                              Thanks for clarification

                              I knew that hg was sometimes haplogroup, but it is also appear as a Human Genome reference, which is what threw me off.

                              This is part of the problem in genetic notations: common symbols have multiple meanings, so that the plus-sign means positive or additional or found in different contexts, and the minus-sign can mean negative, less, or missing.

                              The "older" hierarchical structure is more obvious for analysis, but faces the problems of taking a lot of screen real estate, and in my case, the I haplo being dependent on fonts that clearly distinguish 1 (one) from I (eye) and l (small letter ell) which as you see, this forum font fails the test.

                              Thanks again, you have been a great help as opposed to the frequent condescending replies I have gotten on this forum. I admit I am an contrarian on "origin estimates" and some other questionable claims about DNA. My project is found by searching "Slaton DNA," if you have any suggestions, I am happy to consider them.
                              Last edited by clintonslayton76; 13th February 2018, 06:12 PM.

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                              • #45
                                Forgot to menton...

                                the problem that the connector-dash in, for example, I-F1997, which implies POSITIVE with no other marking. But if the I gets lopped off, it means the opposite, as in NEGATIVE for F1997.
                                This has caused me and many admins to add plus or minus after the SNP as in I-F1997+ and even that seems questionable and confusing since the SNP technically stands alone from the haplotype.
                                This makes for eagle-eyed typing, editing, and reading to avoid "opposite" interpretations, and communications from some admins shows that those who are conversant in SNPs everyday have forgotten about how it was when they were not, and how notes without clear indicators in written-out language make these symbols very confusing.
                                Last edited by clintonslayton76; 15th February 2018, 02:26 PM.

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