A Case for a New A16717 Branch of Hartleys

In my previous Blog on Lawrence’s new BigY test, I mentioned how Lawrence matched Michael on A16717. This was a named SNP that Michael has tested positive for since he took the older BigY500 test.

A16717 at YBrowse

I had shown this graphic in my previou Blog:

The confusing part of this graphic is that even though William Hartley named the SNP as part of R1b, it is also used by YFull in the J-HU209 Branch. If I follow the hyperlink for J-HU209, it brings me to the YFull Tree:

A16717 is shown as a 3/5 star SNP defining J-HU209. I’m not sure how FTDNA deals with SNPs that are in different Haplogroups.

Hartley Testing for A16717

Here is my Block Tree:

The Hartley testers are me and my brother James, then John, Steve, Michael and Lawrence.

As I mentioned Michael tested positive for A16717:

Here are Lawrence’s recent results for the same SNP:

These results go down another page.

Next, I just have to show that the other Hartley testers tested negative for this SNP. Here are John’s results:

His results keep going also.

Here are Steve’s results:

He is also clearly not positive for A16717.

Next, I just need to show that my brother and I are negative for A16717. Here are my brother’s results:

There are no pink A’s under the position for A16717 which indicates that my brother Jim is not positie for A6717.

Lastly, my results:

As expected, the results are the same. I already knew this, but wanted to put the proof out in a Blog.

Blog Update: The Big Tree

I should have checked Alex Williamson’s Big Tree. Michael has his results there. Here is a partial list of Michael’s Unique Mutations:

Here is the explanantion for the codes:

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a “PASS” result with just one possible variant, * indicates a “PASS” but with multiple variants, ** indicates “REJECTED” with just a single variant, and *** indicates “REJECTED” with multiple possible variants. ‘A*’ are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

The CombBED Region

Thanks to the link that Alex Williamson has on his Big Tree page (highlighted above), I now see where this Region is:

This is from Table 1 in the Supplement portion of the article by Adamov. A16717 is between two pages. Here is the Title of the Table:

The HG19 Position for A16717 is 7222463 which is between CombBED Regions 82 and 83. In the Adamov Paper, the CombBED Regions is where Adamov expected his samples to have SNP Variants. However, it appears that Michael and Lawrence had variants in a non-CombBED Region. I don’t know what this means.

Summary and Conclusions

  • This Blog is written to show that clearly Michael and Lawrence are positive for the SNP A16717 and the four other Hartleys are not positive for that SNP
  • I believe that FTDNA should put Michael and Lawrence into their own branch called A16717. This would also support the genealogy which shows Michael and Lawrence as 7th cousins.
  • The only confusing part is that it seems like YFull is using SNP A16717 in a branch of the J Haplogroup.
  • I finally figured out how to figure out where the CombBED Region, thanks to Alex Williamson’s Big Tree Web Site.

 

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