Looking at Stuart’s Big Y-700

I told Stuart (his last name for privacy) that I would look at his Big Y-700. I hesitate to write this Blog, because I am not an expert on Big Y-700 and describing the differences between Stuart’s Big Y-500 and Big Y-700 is likely to be difficult. Stuart is not part of the Frazer YDNA Project that I am part of, but he is in a line that has had a common ancestor with the Frazer’s before the Frazer were Frazer’s. I am also interested in learning about the Big Y-700 as none of the Frazer testers have tested to that level yet. That makes Stuart a pioneer in this area of YDNA testing.

Stuart at YFull

Stuart has uploaded his Big Y-700 and previous Big Y-500 results to YFull. This is helpful in giving probable dates on when the different family lines had their origin. In the big picture, Stuart is R1a.

I see one difference already due to Stuart’s Big Y-700 test. Here are Stuart’s pre-Big Y-700 results:

Before, the number of years to Stuart’s common ancestors were lower. Stuart’s common ancestor with my Frazer relatives used to be 700 years ago. Now it is 800 years ago. Stuart’s common ancestor with his closest group of R-BY26344 used to be 225 years ago. Now it is 425 years ago. That has implications as there is a Stuart and a Grant in that group. The obvious implication is that the mixup in names could have happened up to 200 years further back in time than previously thought.

Stuart’s Big Y at FTDNA

Here is the same tree shown as a block tree at FTDNA but only up to the YP6479 level:

The thing I don’t like about the FTDNA tree is that it filters out too much. For example, I had my Frazer cousin tested shown as YF09981 at YFull above, but he doesn’t show as a match to Stuart at FTDNA. FTDNA shows a stingy 4 Big Y matches for Stuart

By comparison, YFull does a better job at matching SNPs and gives Stuart 71 matches:

More is better. My 2nd cousin with the Irish Flag shows correctly above, ahead of Hayes who has a common ancestor with Stuart of 1150 years ago.

Stuart’s Private Variants at FTDNA

Stuart shows an average of 13 Private Variants with his match Grant above. I would expect that Stuart would have more private variants than Grant as the Big Y-700 is supposed to pick up more than the old Big Y test.

 

This is the first page of Stuart’s Private Variants. He has 19 altogether. These Private Variants are shown above as position numbers. Once they find a match in another Big Y tester, they will be given a name. In order for Stuart and Grant to have an average of 13 Private Variants, Grant must have 7 Private Variants. As there are two in this YP6488 group, it would be helpful to have a third Big Y tester. This additional tester should refine the results in make a new branch for Stuart or Grant.

Tie-Breaking Candidates

Here is a group from the R1a Project:

The two testers with the green R-YP6488 results above are the ones who took the Big Y tests. The other two testers with the red R-M512 results would be the best bets for an additional Big Y test to match with the existing 26 Private Variants to form a new YDNA Branch on the tree of all mankind. I note that the one with the ancestor of Arthur Grant has genealogy that goes back the furthest. However, this is still within the 425 year timeframe for the common ancestor. In other words, there could have been an adoption or other name-changing event before the time of 1683 which separated Stuart from Grant.

Stuart At YFull

Stuart has two kits at YFull.

Big Y-500

I assume the shorter numbered kit is the Big Y-500. Here are Stuart’s 3 Private Variants:

 

This shows on Stuart’s original Big Y-500 test, he had one best quality Novel SNP and two that were acceptable. This SNP has two different position numbers based on the old system (HG19) and the new system (HG38). Due to newer technology and new SNPs being found, there had to be a new numbering system. It appears that this Private Variant already has the name of Y14660. However, different companies may have different names.

Here are the other two  private SNPs or Novel SNPs as YFull calls them:

 

They are of Acceptable quality. The last Novel SNP has a check by it:

It says that someone did a single test for this and it came up negative. Apparently the person who tested for this was someone other than Stuart.

Big Y-700

I’m curious to see any differences here.

Here are some huge differences. Now Stuart is up to 13 Best quality Novel SNPs. I can see the checked SNP from the previous Big Y-500. This has moved up from Acceptable to Best Quality.

Note that 6 Novel SNPs are marked as Homologous. I’m not sure what this means. I think it means that there is a SNP in a totally different haplogroup that looks the same.

One other difference is that YFull used the VCF analysis for Stuart’s Big Y-500. I checked the Big Y-500 test I had done for my Frazer cousin and the BAM file was used for that. My understanding is that the BAM file should be the one to use if possible.

Note that at FTDNA, Stuart had 19 Private Variants. At YFull, Stuart has 13 Novel SNPs of best quality and three of acceptable quality. This seems to be due to differences in how FTDNA and YFull choose which SNPs they should use.

Here is the side by side comparison between YFull and FTDNA:

For the YFull list, I only used the best quality list. That means that there were 7 Best Quality SNPs that YFull found that weren’t used by FTDNA.

Upon further review, I see that FTDNA has a second page of SNP Variants:

 

Now the comparison is closer. FTDNA has 19 Private Variants and YFull shows 15 Novel SNPs that match FTDNA’s. YFull has 13 SNPs of best quality and 3 SNPs of acceptable quality. These private SNPs are measuring Stuart’s non-matchedness. In other words, these are SNPs that are waiting to be matched, so that Stuart can form a new YDNA branch.

When I look at SNPs under different categories at YFull, it adds one SNP that FTDNA had. This brings up the importance of YFull. It is not necessarily showing that FTDNA is wrong but gives a second independent opinion to the analysis of the results.

YFull STR Matching

Here are the results of Stuart’s STR Matching at YFull:

When I try to choose Stuart’s old Big Y test, I get no results, so these are based on the more recent Big Y-700 test. The results are interesting, though generally not as precise as SNP results. Stuart’s closest match is correctly with Grant with a distance 0.03. After that, there are two Frazer’s, a Hayes and another Frazer. The last Frazer with the Irish Flag is my 2nd cousin once removed. Clearly the Hayes connection is much further back than the Frazer connection:

Extended STR Matching at FTDNA

This is available, but not in one place like YFull has it:

Here are Stuart’s 111 STR matches. If they have taken the Big Y test, then those results will show also. YFull showed 5 extended results. These are all the Frazer results. The rest of the group can be found at Stuart’s 67 STR match page:

For whatever reason, my second cousin once removed seems to have more than the average number of mutations, or that STRs that changed were the faster moving STRs to begin with.

Summary and Conclusions

  • Based on YFull, Stuart had a large increase of Private Variants or SNPs between his Big Y-500 and Big Y-700 test. Based on the Big Y-500, Stuart had 3 Private SNPs. This went up to 16 Private SNPs with the Big Y-700 test.
  • Stuart’s original YFull analysis was based on his VCF file and his Big Y-700 YFull analysis is based on his BAM file. My understanding is that the BAM analysis is more detailed.
  • Stuarts dates for a common ancestor to his Grant match and to his Frazer matches increased. This is apparently due to the increase of Stuart’s newly found Private SNPs. The more unmatched SNPs you have, the further you have to a common ancestor.
  • The new date for the common ancestor of 425 years before present between Stuart and Grant has genealogical implications. That goes back to before the year 1600. That means that the mixup between Grant and Stuart could go back that long, or it could be that these surnames were less set in stone at that time.
  • I don’t know how to look at Stuart’s old Big Y-500 results at FTDNA. It doesn’t seem like the old results are kept separately like YFull does.

 

 

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