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Y-DNA Haplogroup Confusion

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  • Armando
    replied
    Originally posted by MMaddi View Post
    As I wrote to you by e-mail, did you check the csv file to make sure that there was a call for U106? If U106 was a "no call," then you are probably U106+. In that case, the Z156 SNP pack would be appropriate for you.

    Don't order any SNP pack until you've seen what call, if any, Geno 2.0 gave you for U106.
    I already know it won't be a no-call. There is always a positive or negative call for U106 in Geno 2.0 files.

    Leave a comment:


  • MMaddi
    replied
    Originally posted by MLT View Post
    While FTDNA is suggesting the R1b - Z156 SNP Pack I agree with Armando and will go with the R1b - M343&M269 Backbone SNP Pack

    My Geno 2.0 test showing positive for FGC11678 is a mystery to me.
    As I wrote to you by e-mail, did you check the csv file to make sure that there was a call for U106? If U106 was a "no call," then you are probably U106+. In that case, the Z156 SNP pack would be appropriate for you.

    Don't order any SNP pack until you've seen what call, if any, Geno 2.0 gave you for U106.

    Leave a comment:


  • MLT
    replied
    Originally posted by Armando View Post
    He really should get the R1b - M343&M269 Backbone SNP Pack or BigY test then he wouldn't have this terminal SNP problem at FTDNA.
    While FTDNA is suggesting the R1b - Z156 SNP Pack I agree with Armando and will go with the R1b - M343&M269 Backbone SNP Pack

    My Geno 2.0 test showing positive for FGC11678 is a mystery to me.

    Leave a comment:


  • Armando
    replied
    Originally posted by MMaddi View Post
    FTDNA is very good at accurate testing, but they do have problems with their haplotree. My understanding is that it's not uncommon for someone who's R1b and transfers their Geno 2.0 results into an FTDNA account to end up with the obviously wrong haplogroup of F-M89. I don't know what the discrepancy is between Geno 2.0's tree and that of FTDNA that causes this.

    Once you received your STR results, FTDNA was able to make a prediction of R-M269. Haplogroup predictions for those without SNP tests at FTDNA (yours are from Geno 2.0) are made based on ths STR results.

    Now, it seems that after further analysis of your Geno 2.0 SNP results (maybe in light of their prediction of R-M269), they've determined that your confirmed haplogroup is R-FGC11678. So, it must be that your Geno 2.0 results have you as FGC11678+.

    You've correctly noted in another thread that FGC11678 is a subclade of U106. More specifically, based on consulting the U106 Project tree, it's a subclade of Z156, a major branch of U106. Please join the R1b-U106 Project at https://www.familytreedna.com/groups/u106/about. We have over 800 Big Y results of project members (about 25% of the total membership) and use a comparison spreadsheet to continually find new subclades. We may be able to place you in a more downstream subclade - FGC11678 has two known subclades (FGC14326 and A5396) - which may not be tested by Geno 2.0.
    He is negative for U106 and therefore there is absolutely no reason for him to join the U106 project. P312 and DF27 are not tested by Geno 2.0 but CTS4528, L238, DF19, L21, U152, and U106 are tested by Geno 2.0. He stated the following in the initial post "I recently transferred my results from the National Geographic Gen 2.0 Test. That test listed my haplogroup as P310." That means he tested negative for U106.

    That leaves very few branches below P310 that Geno 2.0 didn't test that he could be positive for with DF27 being the largest one out of those. The others are DF99, A9063, and a couple more that can be seen at http://www.ytree.net/

    He can verify all of that by downloading the file that shows up in his default page like the one in the example at http://i.imgur.com/gcRTGZr.jpg

    He really should get the R1b - M343&M269 Backbone SNP Pack or BigY test then he wouldn't have this terminal SNP problem at FTDNA.

    Leave a comment:


  • MMaddi
    replied
    Originally posted by MLT View Post
    Ok, I have an update. The F-M89 determination which was obviously not correct was updated by FTDNA. A few days ago after my Y-STP tests came back and co-mingled (I guess), with My Geno 2.0 SNP's they changed me to Haplogroup M-269 which made sense.
    I log in today and it now read Haplogroup R-FGC11678

    Could someone help me understand what that means and why it keeps changing?
    FTDNA is very good at accurate testing, but they do have problems with their haplotree. My understanding is that it's not uncommon for someone who's R1b and transfers their Geno 2.0 results into an FTDNA account to end up with the obviously wrong haplogroup of F-M89. I don't know what the discrepancy is between Geno 2.0's tree and that of FTDNA that causes this.

    Once you received your STR results, FTDNA was able to make a prediction of R-M269. Haplogroup predictions for those without SNP tests at FTDNA (yours are from Geno 2.0) are made based on ths STR results.

    Now, it seems that after further analysis of your Geno 2.0 SNP results (maybe in light of their prediction of R-M269), they've determined that your confirmed haplogroup is R-FGC11678. So, it must be that your Geno 2.0 results have you as FGC11678+.

    You've correctly noted in another thread that FGC11678 is a subclade of U106. More specifically, based on consulting the U106 Project tree, it's a subclade of Z156, a major branch of U106. Please join the R1b-U106 Project at https://www.familytreedna.com/groups/u106/about. We have over 800 Big Y results of project members (about 25% of the total membership) and use a comparison spreadsheet to continually find new subclades. We may be able to place you in a more downstream subclade - FGC11678 has two known subclades (FGC14326 and A5396) - which may not be tested by Geno 2.0.

    Leave a comment:


  • MLT
    replied
    Ok, I have an update. The F-M89 determination which was obviously not correct was updated by FTDNA. A few days ago after my Y-STP tests came back and co-mingled (I guess), with My Geno 2.0 SNP's they changed me to Haplogroup M-269 which made sense.
    I log in today and it now read Haplogroup R-FGC11678

    Could someone help me understand what that means and why it keeps changing?

    Leave a comment:


  • MLT
    replied
    Originally posted by Darren View Post
    Hello MLT,

    Can you please send me a private message with your kit number and a contact email address? I will try and get the ticket addressed.

    -Darren
    Family Tree DNA
    That would be much appreciated Darren.
    PM sent with requested info.

    Leave a comment:


  • Darren
    replied
    Hello MLT,

    Can you please send me a private message with your kit number and a contact email address? I will try and get the ticket addressed.

    -Darren
    Family Tree DNA

    Leave a comment:


  • MLT
    replied
    Originally posted by Armando View Post
    That's enough to prove without a doubt that you belong to an R1b-P310 subclade because none of those are false positives and you are also positive for SNPs upstream from P310.
    Thanks for the confirmation. Now I have to wonder if anyone from FTDNA will ever respond to the ticket I opened.
    Would be nice to get the F-M89 result corrected.

    Thanks again for all of the help and leading me to a better understanding.

    Leave a comment:


  • Armando
    replied
    Originally posted by MLT View Post
    Below are the results from your list above.

    M343 R1b (+)
    YSC0000224 R1b1a (+)
    PF6498 R1b1a1a (+)
    CTS11985 R1b1a1a (+)
    L502 R1b1a1a (+)
    L483 R1b1a1a2 (+)
    L762 R1b1a1a2 (+)
    CTS3475 R1b1a1a2 (+)
    s3 R1b1a1a2 (+)
    PF6265 R1b1a1a2 (+)
    YSC0000225 R1b1a1a2 (+)
    L23 R1b1a1a2a (+)
    YSC0000191 R1b1a1a2a1a (+)
    P310 R1b1a1a2a1a (+)
    L52 R1b1a1a2a1a (+)
    YSC0000082 R1b1a1a2a1a (+)
    That's enough to prove without a doubt that you belong to an R1b-P310 subclade because none of those are false positives and you are also positive for SNPs upstream from P310.

    If you download the CSV file such as seen in the screenshot at http://i.imgur.com/gcRTGZr.jpg then open that file and look for the following SNPs and check the alleles then look up the SNPs and the allele_anc in the CSV file at http://ybrowse.org/gbrowse2/gff/ you will see that you have the ancestral allele for CTS4528, L238, DF19, L21, U152, and U106 meaning that you are negative for those SNPs. That leaves very few branches below P310 that Geno 2.0 didn't test that you could be positive for with DF27 being the largest one out of those. The others are DF99, A9063, and a couple more that can be seen at http://www.ytree.net/ which are also at http://www.ytree.net/DisplayTree.php?blockID=1560 and http://www.ytree.net/DisplayTree.php?blockID=202

    Leave a comment:


  • MLT
    replied
    Originally posted by Armando View Post

    F-M89 is definitely not correct. No question.

    Your haplotree page should also show you positive for the following SNPs from the Geno 2.0 test -

    SNP Longhand
    M343 R1b
    CTS2134 R1b1
    YSC0000224 R1b1a
    PF6498 R1b1a1a
    CTS11985 R1b1a1a
    L502 R1b1a1a
    L483 R1b1a1a2
    L762 R1b1a1a2
    CTS3475 R1b1a1a2
    s3 R1b1a1a2
    CTS4608 R1b1a1a2
    PF6265 R1b1a1a2
    YSC0000225 R1b1a1a2
    L23 R1b1a1a2a
    L51 R1b1a1a2a1
    YSC0000191 R1b1a1a2a1a
    P310 R1b1a1a2a1a
    L52 R1b1a1a2a1a
    YSC0000082 R1b1a1a2a1a
    L253 R1b1a1a2a1a2~
    L326 R1b1a1a2a1a2~
    CTS4528 R1b1a1a2a1a3a

    Below are the results from your list above.

    M343 R1b (+)
    CTS2134 R1b1 (?) Not shown in positive test results
    YSC0000224 R1b1a (+)
    PF6498 R1b1a1a (+)
    CTS11985 R1b1a1a (+)
    L502 R1b1a1a (+)
    L483 R1b1a1a2 (+)
    L762 R1b1a1a2 (+)
    CTS3475 R1b1a1a2 (+)
    s3 R1b1a1a2 (+)
    CTS4608 R1b1a1a2 (?) Not shown in positive test results
    PF6265 R1b1a1a2 (+)
    YSC0000225 R1b1a1a2 (+)
    L23 R1b1a1a2a (+)
    L51 R1b1a1a2a1 (?) Not shown in positive test results
    YSC0000191 R1b1a1a2a1a (+)
    P310 R1b1a1a2a1a (+)
    L52 R1b1a1a2a1a (+)
    YSC0000082 R1b1a1a2a1a (+)
    L253 R1b1a1a2a1a2~ (+)
    L326 R1b1a1a2a1a2~ Not shown in positive test results
    CTS4528 R1b1a1a2a1a3a Not shown in positive test result

    Leave a comment:


  • Armando
    replied
    Originally posted by Armando View Post
    L253 R1b1a1a2a1a2~
    L326 R1b1a1a2a1a2~
    CTS4528 R1b1a1a2a1a3a
    I accidentally included these three in my previous post. You will possibly be positive for L253 and L326 only if you belong to a P312 subclade. CTS4528 shouldn't be in your list of positive SNPs although it is possible.

    Leave a comment:


  • MLT
    replied
    Originally posted by Armando View Post
    Whit Athey's halpogroup predictor is based on STR markers. You already have your STR results?

    F-M89 is definitely not correct. No question.
    No, I don't have STR results yet. I am quite new at this and appreciate the patience being shown. Just when I thought I had it figured out looks like maybe not. Interesting though that when I entered the positive SNP's from Gen 2.0 into the predictor it did give a full list of probability percentages rather than some kind of error message.
    I will check to see if the SNP's you mentioned show positive.

    Leave a comment:


  • Armando
    replied
    Originally posted by MLT View Post
    I ran the raw data received from Gen 2.0 via FTDNA through Whit Athey's halpogroup predictor. The results were 67.4% for R1b. (the next closest was 11%). This should confirm the Gen 2.0 findings of P310+ and M269.
    I have opened a ticket with FTDNA to try and clear up their finding of F-M89 which simply cannot be correct.

    Thanks for all of the help.
    Whit Athey's halpogroup predictor is based on STR markers. You already have your STR results?

    F-M89 is definitely not correct. No question.

    Your haplotree page should also show you positive for the following SNPs from the Geno 2.0 test -

    SNP Longhand
    M343 R1b
    CTS2134 R1b1
    YSC0000224 R1b1a
    PF6498 R1b1a1a
    CTS11985 R1b1a1a
    L502 R1b1a1a
    L483 R1b1a1a2
    L762 R1b1a1a2
    CTS3475 R1b1a1a2
    s3 R1b1a1a2
    CTS4608 R1b1a1a2
    PF6265 R1b1a1a2
    YSC0000225 R1b1a1a2
    L23 R1b1a1a2a
    L51 R1b1a1a2a1
    YSC0000191 R1b1a1a2a1a
    P310 R1b1a1a2a1a
    L52 R1b1a1a2a1a
    YSC0000082 R1b1a1a2a1a
    L253 R1b1a1a2a1a2~
    L326 R1b1a1a2a1a2~
    CTS4528 R1b1a1a2a1a3a

    Leave a comment:


  • MLT
    replied
    Update

    I ran the raw data received from Gen 2.0 via FTDNA through Whit Athey's halpogroup predictor. The results were 67.4% for R1b. (the next closest was 11%). This should confirm the Gen 2.0 findings of P310+ and M269.
    I have opened a ticket with FTDNA to try and clear up their finding of F-M89 which simply cannot be correct.

    Thanks for all of the help.

    Leave a comment:

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