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  • #31
    Originally posted by MMaddi View Post

    Remember that Geno 2.0 has about 10,000 new yDNA SNPs never tested before by any commercial company. Only after they look at thousands of results for these new SNPs will they be able to accurately place the SNPs on the tree and have permanent long names.
    This question might have an obvious answer but I'll ask it anyway; how did they discover these new snp's exactly?

    Comment


    • #32
      Originally posted by brenden View Post
      This question might have an obvious answer but I'll ask it anyway; how did they discover these new snp's exactly?
      They were discovered by scientists in their studies, but never tested in a wide public sample. Here's a link to some information on the CTS (Chris Tyler Smith), F (Li Jin from Fudan University) and PF (Paolo Francalacci) SNPs - http://www.isogg.org/wiki/Genographic_Project#Y-DNA

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      • #33
        Originally posted by MMaddi View Post
        They were discovered by scientists in their studies, but never tested in a wide public sample. Here's a link to some information on the CTS (Chris Tyler Smith), F (Li Jin from Fudan University) and PF (Paolo Francalacci) SNPs - http://www.isogg.org/wiki/Genographic_Project#Y-DNA
        Thanks, that gives me a better picture of whats going on.

        Comment


        • #34
          Confused?

          On my FTDNA page these results show-up for my SNP's tested. I am I-Z138.

          Z148+ Z139+ Z138+ V9+ V205+ V189+ V186+ PAGES00123+ P30+ P187+ P166+ P160+ P159+ P158+ P151+ P148+ P146+ P145+ P141+ P14+ P138+ P136+ P135+ P130+ P127+ P126+ P124+ P123+ M94+ M89+ M450+ M42+ M307+ M294+ M170+ M168+ M139+ L80+ L75+ L594+ L578+ L575+ L574+ L566+ L552+ L517+ L516+ L515+ L509+ L498+ L493+ L477+ L470+ L468+ L403+ L366+ L350+ L187+ L16+ L157+ L15+ L132+ L125+ L124+ L121+ L118+

          Are these the ones I tested positive for or just the ones tested generally.

          Because I got some SNP's for hg R, E, and I (even IJK and IJ - but that make sense). I do not see how that can be.

          Then one of the SNPs is PAGE123 which on the tree says 'I (notes)'. OK!

          The note says: •Page123: The precise location of Page123 is uncertain. It is derived in four men with Haplogroup I1 SNPS and ancestral for one man in Haplogroup J. It has not been tested in Haplogroup I2.

          What's up? Me confused!

          Comment


          • #35
            Originally posted by JTR View Post
            On my FTDNA page these results show-up for my SNP's tested. I am I-Z138.

            Z148+ Z139+ Z138+ V9+ V205+ V189+ V186+ PAGES00123+ P30+ P187+ P166+ P160+ P159+ P158+ P151+ P148+ P146+ P145+ P141+ P14+ P138+ P136+ P135+ P130+ P127+ P126+ P124+ P123+ M94+ M89+ M450+ M42+ M307+ M294+ M170+ M168+ M139+ L80+ L75+ L594+ L578+ L575+ L574+ L566+ L552+ L517+ L516+ L515+ L509+ L498+ L493+ L477+ L470+ L468+ L403+ L366+ L350+ L187+ L16+ L157+ L15+ L132+ L125+ L124+ L121+ L118+

            Are these the ones I tested positive for or just the ones tested generally.

            Because I got some SNP's for hg R, E, and I (even IJK and IJ - but that make sense). I do not see how that can be.

            Then one of the SNPs is PAGE123 which on the tree says 'I (notes)'. OK!

            The note says: •Page123: The precise location of Page123 is uncertain. It is derived in four men with Haplogroup I1 SNPS and ancestral for one man in Haplogroup J. It has not been tested in Haplogroup I2.

            What's up? Me confused!
            What seems to be the case for those who've uploaded their Geno 2.0 yDNA results into their FTDNA accounts is that only some of their positive results will show up there. What shows up in your account are all positive and negative SNP results from testing by FTDNA and positive and negative results for those yDNA SNPs tested by Geno 2.0 that are also on FTDNA's testing menu.

            Suppose you test positive for a Z SNP on the Geno 2.0 that is not available for testing yet at FTDNA. Even though you tested positive for this SNP on Geno 2.0, it will not show up on your Haplotree page with other SNP results.

            If you belong to a project that has its SNP page turned on to display on its public website, you will see all your results from SNP testing by FTDNA and all positive SNP results from Geno 2.0 testing. You will not see any negative results from Geno 2.0 testing there because there are 12,000 SNPs on the chip and they don't have the space to list negative results.

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            • #36
              Originally posted by JTR View Post
              Are these the ones I tested positive for or just the ones tested generally.
              Because I got some SNP's for hg R, E, and I (even IJK and IJ - but that make sense). I do not see how that can be.
              Yes, you tested positive for all of those. This is actually only a subset of your positive SNPs, though -- the Haplotree page doesn't yet recognize all the new SNPs that start with CTS, PF, F and some other prefixes. If you are in a project that has the SNP report enabled on the project's public website, look yourself up there and you'll see your complete list of positive SNPs.

              Some SNPs happened more than once in different haplogroups. There may also be some cases of SNPs that are not behaving properly and have erroneous results -- this unfortunately can happen with SNP chip technology. We'll have to wait until we have more info on each of the SNPs to see what the situation is.

              Elise

              Comment


              • #37
                Originally posted by MMaddi View Post
                What seems to be the case for those who've uploaded their Geno 2.0 yDNA results into their FTDNA accounts is that only some of their positive results will show up there. What shows up in your account are all positive and negative SNP results from testing by FTDNA and positive and negative results for those yDNA SNPs tested by Geno 2.0 that are also on FTDNA's testing menu.
                ...
                Unfortunately, this is not the case. I have zero negative results showing for any of the SNPs that are in my Geno 2.0 raw data, and that are in FTDNA's testing menu.

                e.g., DF23, M222, ...

                Comment


                • #38
                  Originally posted by ScooterCat View Post
                  Unfortunately, this is not the case. I have zero negative results showing for any of the SNPs that are in my Geno 2.0 raw data, and that are in FTDNA's testing menu.

                  e.g., DF23, M222, ...
                  This seems to be the case - I joined a couple of Projects and all my SNPs (430+) are plus and no negatives.

                  I am still concerned why I have some SNPs that belong to other Hgs. Like L$77 and L493 for R1b>; L366 for R1a>; L515, L516, L517 for E1b> and few being investigated under R1b. And that was just from a shorter list of 66 that FTDNA first put up.

                  Also, if only four or five people have teste d for one of these in that a private SNP of some other catergory below that?

                  Comment


                  • #39
                    Originally posted by JTR View Post
                    Like L$77
                    That SNP helps you make a lot of money ---- or is it the other way around.

                    Comment


                    • #40
                      Originally posted by ScooterCat View Post
                      Unfortunately, this is not the case. I have zero negative results showing for any of the SNPs that are in my Geno 2.0 raw data, and that are in FTDNA's testing menu.

                      e.g., DF23, M222, ...
                      If you're referring to negative results, as you described above, not showing up on your Haplotree page, then I guess I was mistaken. (We're all still trying to figure out what's happening. I'm not sure that FTDNA knows yet.) Or are you referring to negative results from Geno 2.0 not showing up on SNP page of the project you're a member of? If that's the case, that's exactly what I wrote in my third paragraph, which you didn't quote:

                      "If you belong to a project that has its SNP page turned on to display on its public website, you will see all your results from SNP testing by FTDNA and all positive SNP results from Geno 2.0 testing. You will not see any negative results from Geno 2.0 testing there because there are 12,000 SNPs on the chip and they don't have the space to list negative results."

                      Comment


                      • #41
                        Originally posted by MMaddi View Post
                        If you're referring to negative results, as you described above, not showing up on your Haplotree page, then I guess I was mistaken. (We're all still trying to figure out what's happening. I'm not sure that FTDNA knows yet.) Or are you referring to negative results from Geno 2.0 not showing up on SNP page of the project you're a member of? If that's the case, that's exactly what I wrote in my third paragraph, which you didn't quote:

                        "If you belong to a project that has its SNP page turned on to display on its public website, you will see all your results from SNP testing by FTDNA and all positive SNP results from Geno 2.0 testing. You will not see any negative results from Geno 2.0 testing there because there are 12,000 SNPs on the chip and they don't have the space to list negative results."
                        Are you saying that Geno presents to FTDNA also the negatives.......in which case you should not need to do SNP ( IF FTDNA show them ) as they will be shown in FTDNA.
                        or
                        Is FTDNA going to hide them and wait for you to do a SNP test....and then .....

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                        • #42
                          There are no negative results anywhere.

                          Comment


                          • #43
                            Originally posted by Bartot View Post
                            Are you saying that Geno presents to FTDNA also the negatives.......in which case you should not need to do SNP ( IF FTDNA show them ) as they will be shown in FTDNA.
                            or
                            Is FTDNA going to hide them and wait for you to do a SNP test....and then .....
                            Are you seriously suggesting that FTDNA should display results for 12,000 SNPs in your account or on the SNP pages of projects? Do you realize what that would do to their servers and database?

                            Every one who has Geno 2.0 results is given their raw data, whether they upload those results to FTDNA or not. So, you can look up the results yourself for all SNPs, positive and negative.

                            However, it is a tedious process to interpret the results, because my understanding is that Geno 2.0 doesn't tell you if you're derived (positive) or ancestral (negative). They tell you what base (A, C, G or T) was read for each SNP. You'd have to look up whether your base is derived or ancestral for each SNP.

                            This is why various administrators of haplogroup projects are collecting Geno 2.0 results from their members. They have some idea of how to interpret Geno 2.0 results and also are comparing results submitted by various members to locate new SNPs and subclades. That's the only way to do it effectively. If people are just looking at their own results without comparing to others, there's no way to tell if someone has a private SNP, is part of a new subclade or has a false positive. Ultimately, it will take analysis by Spencer Wells and the other scientists who have all Geno 2.0 results at their disposal to draw a new tree, but knowledgeable genetic genealogists can contribute to that process by working together in comparing results now.
                            MMaddi
                            yDNA: R-CTS2509; mtDNA: T2e
                            Last edited by MMaddi; 16 December 2012, 01:27 AM.

                            Comment


                            • #44
                              Originally posted by MMaddi View Post
                              Are you seriously suggesting that FTDNA should display results for 12,000 SNPs in your account or on the SNP pages of projects? Do you realize what that would do to their servers and database?

                              Every one who has Geno 2.0 results is given their raw data, whether they upload those results to FTDNA or not. So, you can look up the results yourself for all SNPs, positive and negative.

                              However, it is a tedious process to interpret the results, because my understanding is that Geno 2.0 doesn't tell you if you're derived (positive) or ancestral (negative). They tell you what base (A, C, G or T) was read for each SNP. You'd have to look up whether your base is derived or ancestral for each SNP.

                              This is why various administrators of haplogroup projects are collecting Geno 2.0 results from their members. They have some idea of how to interpret Geno 2.0 results and also are comparing results submitted by various members to locate new SNPs and subclades. That's the only way to do it effectively. If people are just looking at their own results without comparing to others, there's no way to tell if someone has a private SNP, is part of a new subclade or has a false positive. Ultimately, it will take analysis by Spencer Wells and the other scientists who have all Geno 2.0 results at their disposal to draw a new tree, but knowledgeable genetic genealogists can contribute to that process by working together in comparing results now.
                              no, I am saying that if you transfer from NG to FTDNA, then Ftdna should advise someone where a SNP is a negative because it was tested under NG.

                              example, below my positive L446 is L447, if I did the NG test and it was transfered to Ftdna, then I would highly presume that L447 was tested. Since in 100% of all positive L446 tested are found negative L447 ( so far ) , then If I inquire ( or my project manager) to Ftdna to run a L447 test, Ftdna should advise ( with integrity ) it was already done and the result was ...whatever...without a fee.

                              My understanding is that NG results are presented in rs numbers and not all SNPs have rs numbers ...at this time.

                              As per comment below made by experienced scholars of genetics
                              Of the SNPs in the Geno 2.0 test, there are approximately four hundred SNPs in the y-chromosome that are derived (rather than ancestral) that have so far been seen in at least some haplogroup I1 people. Most of those SNPs will probably be phyloequivalent to the SNPs given in the I1 SNP tree pathway shown above. But there are still a few interesting Geno 2.0 SNP alleles that may be important to haplogroup I1 people. They are:

                              F1583+, found in an P109+ person.
                              F2642+, found in an Z140+ person.
                              F3312+, found in an M253+, but Z58-, Z63-, Z131- person.
                              CTS7362+, CTS9352+, CTS9477+, found in a single L573+ person.
                              YSC0000261+, found in three separate Z140+ people.
                              CTS8647+, found in the same three people as YSC0000261+, and also in another Z140+ person, a L573+ person, and a Z60+ person.
                              It would seem , by your comments and the comments made by NG, that NG are far more interested in the ( negative , as you put it ) ancestral , so advising the tested of the negative would be paramount as that is the whole purpose of what NG 2.0 was set up to do. It was not a test to find family members from the past.

                              to me, NG is basically a test of one's auDNA signals as being more important and less so to yDNA and mtDNA
                              Bartot
                              FTDNA Customer
                              Last edited by Bartot; 16 December 2012, 12:57 PM.

                              Comment


                              • #45
                                Interpreting my raw data: Help!

                                Below is my interpretation of my Geno 2.0 raw data, based on the ISOGG YDNA SNP index for 2012. It's a mess. It seems that I have derived mutations on 3 separate branches of the R-L21 derived SNP tree plus 2 SNPs that are neither derived nor ancestral (L371 and L720). My hope is that I am misinterpreting the data. For the derived (and the unknown) SNPs, I've noted the ancestral and derived nucleotide (as shown by the ISOGG YDNA SNP index). Have I misinterpreted the raw data? It's very possible. In fact, I hope that I have.

                                http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

                                David Reynolds has created a nice diagram of the ISOGG L21 SNPs.

                                http://eng.molgen.org/viewtopic.php?f=122&t=723

                                I inserted (DF13+) (DF49+), which are not included on the chip used by Geno 2.0, because (DF13+) lies between L21and the SNPs listed and (DF49+) lies between L21 and DF23 on the tree of ISOGG SNPs derived from L21+ (but based on my results who knows, perhaps they would have been ancestral).

                                GRC12124452_ChipNGv1_37946_F03,L21,Y,G,G L21+ C->G

                                GRC12124452_ChipNGv1_37946_F03,M37,Y,T,T L21+ (DF13+) M37+ C->T
                                GRC12124452_ChipNGv1_37946_F03,L96,Y,A,A
                                GRC12124452_ChipNGv1_37946_F03,L144,Y,A,A
                                GRC12124452_ChipNGv1_37946_F03,L371,Y,A,A L371+ = T->G
                                GRC12124452_ChipNGv1_37946_F03,L555,Y,G,G
                                GRC12124452_ChipNGv1_37946_F03,Z255,Y,T,T
                                GRC12124452_ChipNGv1_37946_F03,L513,Y,C,C
                                GRC12124452_ChipNGv1_37946_F03,Z253,Y,G,G
                                GRC12124452_ChipNGv1_37946_F03,DF21,Y,C,C

                                GRC12124452_ChipNGv1_37946_F03,L706,Y,A,A L21+ (DF13+) L513- L706.2+ G->A
                                GRC12124452_ChipNGv1_37946_F03,P66_1,Y,G,G
                                GRC12124452_ChipNGv1_37946_F03,DF23,Y,A,A L21+ (DF13+) (DF49+) DF23+ G->A
                                GRC12124452_ChipNGv1_37946_F03,L226,Y,C,C
                                GRC12124452_ChipNGv1_37946_F03,L554,Y,A,A
                                GRC12124452_ChipNGv1_37946_F03,L643,Y,C,C
                                GRC12124452_ChipNGv1_37946_F03,P314,Y,T,T
                                GRC12124452_ChipNGv1_37946_F03,Z246,Y,T,T
                                GRC12124452_ChipNGv1_37946_F03,L720,Y,C,C L720+ = G->T
                                GRC12124452_ChipNGv1_37946_F03,L744,Y,C,C

                                GRC12124452_ChipNGv1_37946_F03,L705,Y,T,T L21+ (DF13+) L513- L706.2+ L705.2+ G->T
                                GRC12124452_ChipNGv1_37946_F03,M222,Y,A,A L21+ (DF13+) (DF49+) DF23+ M222+ G->A
                                GRC12124452_ChipNGv1_37946_F03,DF25,Y,C,C

                                GRC12124452_ChipNGv1_37946_F03,DF5,Y,A,A

                                GRC12124452_ChipNGv1_37946_F03,L627,Y,T,T
                                kullfarr
                                Registered User
                                Last edited by kullfarr; 16 December 2012, 01:56 PM. Reason: typo

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