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Thread: Z18133 results in Geno 2.0 NG tests - possible false positives

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    Z18133 results in Geno 2.0 NG tests - possible false positives

    Based on two examples in my R-ZZ10 project, I now have a strong suspicion that anyone who is listed as R-Z18133 (which is several levels below Z253 in reality) based *solely* on Geno 2.0 NG testing is likely to be an incorrect place on the haplotree.

    N193040 - the next SNP up the haplotree that shows as tested positive is L21; an exact 37-marker match with the same surname and contact email (who is also in the project) has been confirmed as Z253- by both the R1b Backbone and L21 SNP Packs.

    477741 - the next SNP up the haplotree that shows as tested positive is L51 (he has P310 in the raw results as well); unfortunately, this man has a fairly vanilla R1b haplotype and has only tested 25 markers, so I don't have any informed guesses from STR patterns as to what his actual SNP grouping might be.

    I logged a ticket to FTDNA to have them look at those two results.

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    I'm not showing Z18133 to be a false positive in the NextGen results of a U106 or of a HG-I person. It doesn't surprise me though that there are people that are positive by chance for an individual SNP and are assigned that subclade even though their upstream SNPs show they are negative for them. It's still weird that you have two participants with false positives but I have two files that don't.

    Have you downloaded their Y-DNA SNPs as CSV using the link as shown in the following screenshot?



    Once you download the CSV file you can search for the results of Z18133 and Z253 and see if they are ancestral for both Z18133 and Z253 or just Z253. CTS1751 and L21 are also tested by Geno 2.0 NG.

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    Thanks! As I've never had any Geno 2.0 testing myself, I didn't realize that there was *another* raw data file to download immediately below the SNP download link in the Y-DNA section. I've downloaded the .csv files for both.

    The file for 477741 is completely blank, unfortunately, so I don't have anything more to go on for him. However, the file for N193040 has SNP calls in it. Z18133 has the ancestral call of G there, as does Z253 (which is also G), so in that case the error seems to be fairly clearly in the FTDNA interpretation of the Geno 2.0 NG results.
    Last edited by swid; 09-12-2016 at 09:09 PM.

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    Simply looking at my project's SNP report, I see about 20 false Z18133+ results:
    #B79612, I-CTS1846
    #354451, I-Y3548
    #N163095, I-Z187
    #N153825, J-L816
    #N212163, J-Z600
    etc.

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    Quote Originally Posted by lgmayka View Post
    Simply looking at my project's SNP report, I see about 20 false Z18133+ results:
    #B79612, I-CTS1846
    #354451, I-Y3548
    #N163095, I-Z187
    #N153825, J-L816
    #N212163, J-Z600
    etc.
    If you download their CSV files they probably have G in their raw data.

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    Quote Originally Posted by swid View Post
    Thanks! As I've never had any Geno 2.0 testing myself, I didn't realize that there was *another* raw data file to download immediately below the SNP download link in the Y-DNA section. I've downloaded the .csv files for both.

    The file for 477741 is completely blank, unfortunately, so I don't have anything more to go on for him. However, the file for N193040 has SNP calls in it. Z18133 has the ancestral call of G there, as does Z253 (which is also G), so in that case the error seems to be fairly clearly in the FTDNA interpretation of the Geno 2.0 NG results.
    I looked at the SNP page of the projects the people whose files I had looked at, that that have G in their raw data files, and they also show to be Z18133+. The DF27 SNP page also shows a lot of people with Z18133+ and they are probably also Geno 2.0 NG customers.

    Most of the time that I have seen false positives it has been in the raw data and not solely in the SNP report page. I have been complaining for a long time about FTDNA not getting the negative calls from Geno 2.0 and that causing an incorrect placement of people into a subclade they don't belong in. I wish Geno 2.0 and FTDNA would collaborate a lot more on getting the problems fixed. It seems as though they need a programmer dedicated to creating an algorithm that sorts the results correctly based on both positives and negatives and filters out the false positives based on them being found in results from many different haplogroups.

    I wonder how many other SNPs that are negative in the Geno 2.0 NG raw data are shown as positives at FTDNA. Your project seems to be affected the most due to L21 being positive.

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    One step forward, one step back.

    N193040 now displays as being R-S7123 (which is an SNP in the L193 block). The S7123 mutation is A-> G; he has a C call in the raw data. He also has a negative call for Z16332 and a C call for the G -> A mutation for S5992 (both of which are also in the block). Of course, he's also ancestral for other SNPs going upstream towards L513.

    Geno 2.0 results are a mess.

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    N193040 is my father's kit (I'm N129953, ZZ10_1), and I was understandably a bit perplexed when I transferred his data over from NatGeo. It's good (figuratively speaking) to now know that this discrepancy isn't just an isolated incident, but a known issue with Geno 2.0 NG interpretation results that can possibly (hopefully) be remedied in the future. My plan is to continue testing his kit as finances allow, but I wonder if it's more feasible to wait and see if this issue gets corrected first.
    Thoughts?

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    Quote Originally Posted by SteveJ View Post
    N193040 is my father's kit (I'm N129953, ZZ10_1), and I was understandably a bit perplexed when I transferred his data over from NatGeo. It's good (figuratively speaking) to now know that this discrepancy isn't just an isolated incident, but a known issue with Geno 2.0 NG interpretation results that can possibly (hopefully) be remedied in the future. My plan is to continue testing his kit as finances allow, but I wonder if it's more feasible to wait and see if this issue gets corrected first.
    Thoughts?
    Steve, I'm the admin of the R-ZZ10 project; I'm glad you showed up on here to clarify the relationship among those kits. Welcome!

    Hopefully FTDNA will get their act together on this; it may help for you to log a ticket to their help desk as well. Since Geno 2.0 NG results don't include DF13 (I think), your father's results should display as R-L21 when they get everything sorted out.

    In any case, since you already know you're ZZ10+ and Z253-, Z255-, CTS3386-, and MC14- from your own results, there's not a whole lot left to test for either one of you. For selfish reasons, I'm curious if you'd turn out to be a member of my own subclade -- BY4046. At this time, the only way to find that out would be to order a Big Y or Full Genomes test (either of which is pretty expensive, but would basically be the last test you'd ever need to order for either kit) or to order BY4047 (which is in the same block as BY4046) from YSEQ. If you've never tested there, the total cost of that would be $22.50.

    Finally, if you simply want your father's FTDNA results to match up with yours, you can order R-ZZ10_1 as a standalone SNP test for $39.

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    I have a member who has been tested with Geno 2, and was CTS11751+. He matches a CTS1751 cluster so have no reason to think he isn't.
    His kit was batched to the lab this week for Big Y testing. Today he shows as R-S7123.
    I take it that this is some sort of glitch with FTDNA system.

    His BIg Y test is still showing awaiting results.

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