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  #1  
Old 17th December 2016, 03:01 AM
MLT MLT is offline
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Y-DNA Haplogroup Confusion

I recently transferred my results from the National Geographic Gen 2.0 Test. That test listed my haplogroup as P310.
It seems strange if I did not have any SNPs downstream of P310. After the transfer it only became more strange, FTDNA has changed my haplogroup to F-M89. If I really am P310, then the FTDNA classification taken from the same test results with a new classification of 'F-M89' doesn't make any sense.
I have a Y-DNA 37 test in progress. Will this clear up the haplogroup issue?
It seems I am spending a lot of money and getting very few answers. Any advice or explanations would be greatly appreciated
Thanks in advance.
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  #2  
Old 17th December 2016, 06:16 AM
Jim Barrett Jim Barrett is offline
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Adding the additional markers will not change your Haplogroup.

When you go to your "Y-DNA Haplogroup & SNP" page there should be a list of your SNP results at the bottom of the page. Is P310 included and if it is, is it + or -?

On the same page, up at the top right of the Haplotree chart there is a search box. Enter P310 in it and click on "Search". Is P310 found? If so what color is it?

ISOGG doesn't include P310 in their F Haplogroup list -
http://isogg.org/tree/ISOGG_HapgrpF.html
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  #3  
Old 17th December 2016, 02:32 PM
lgmayka lgmayka is offline
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You are very likely to belong to R1b-P310 or one of its subclades (like R1b-DF27). When your 37 markers arrive, join the R1b Project.
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  #4  
Old 17th December 2016, 05:32 PM
Armando Armando is offline
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Quote:
Originally Posted by MLT View Post
I recently transferred my results from the National Geographic Gen 2.0 Test. That test listed my haplogroup as P310.
It seems strange if I did not have any SNPs downstream of P310.
The reason that you did not have any downstream SNPs is because Geno 2.0 tests a limited number of SNPs. It does not test P312, DF27, and many other SNPs that are included in the R1b - M343&M269 Backbone SNP Pack. It also means that you are negative for Z195 since that SNP is included in the Geno 2.0 test. If you were to get SNP Packs or BigY then you would find your terminal SNP below P310.


Quote:
Originally Posted by MLT View Post
After the transfer it only became more strange, FTDNA has changed my haplogroup to F-M89. If I really am P310, then the FTDNA classification taken from the same test results with a new classification of 'F-M89' doesn't make any sense.
The Geno 2.0 test has a lot of false positives and false negatives which causes FTDNA to get confused and provide the incorrect terminal SNP after the transfer from Geno 2.0. P310 is not one of the false positive or false negative SNPs through Geno 2.0 so you were given the correct terminal SNP at Geno 2.0 and it will show up as positive at the bottom of https://www.familytreedna.com/my/y-dna-haplotree. If you download the Genographic Y-DNA SNPs as a CSV file on your default page after logging in such as seen in the screenshot at http://i.imgur.com/gcRTGZr.jpg then you can see that P312 and DF27 are not in the list and also that you have G for the Z195 allele which means that you are negative for it. If you would have had A you would have been positive. If you upload the file to a file sharing site and send me the link to the file I can run it through a spreadsheet that compares the CSV file with a CSV file from Ybrowse and reports the longhand HG name of each SNP and your positive and negative results along with the source info and which SNPs are false positives. The FTDNA haplotree page only provides the positive results and includes false positives.

Quote:
Originally Posted by MLT View Post
I have a Y-DNA 37 test in progress. Will this clear up the haplogroup issue?
The Y-DNA 37 test does not provide a haplogroup other than a predicted one such as M269. You already know that you are M269 since you are P310 at Geno 2.0. However, it might cause FTDNA to rerun your Geno 2.0 results but that is just a guess. You would have to ask FTDNA that question by creating a ticket. If you have a close match at 37 markers and that person has had advanced SNP testing at FTDNA then there is a possibility but not a guarantee that you belong to the same terminal SNP as that person. Sometimes, but rarely, there are STRs that will put you into a specific subclade after an analysis by a haplogroup admin, not what FTDNA itself assigns, and then you can get an SNP pack that is more appropriate than the general R1b - M343&M269 Backbone SNP Pack and could save you money.

Quote:
Originally Posted by MLT View Post
It seems I am spending a lot of money and getting very few answers. Any advice or explanations would be greatly appreciated
Thanks in advance.
To begin with Geno 2.0 test was not a good choice for getting the most up-to-date Y-DNA testing.

Last edited by Armando; 17th December 2016 at 05:34 PM.
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  #5  
Old 17th December 2016, 07:01 PM
MLT MLT is offline
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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.
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  #6  
Old 17th December 2016, 08:47 PM
Armando Armando is offline
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Quote:
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
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  #7  
Old 18th December 2016, 01:35 AM
MLT MLT is offline
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Quote:
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.
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  #8  
Old 18th December 2016, 02:17 AM
Armando Armando is offline
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Quote:
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.
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  #9  
Old 18th December 2016, 02:30 AM
MLT MLT is offline
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Quote:
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
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  #10  
Old 18th December 2016, 08:22 AM
Armando Armando is offline
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Quote:
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
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