Getting Ready for BigY 700 Results

According to Family Tree DNA (FTDNA) my BigY 700 results are in, but it appears that the analysis has not completed.

I am told that it can take two weeks to perform a manual analysis once the results are in. The good news is that FTDNA does this analysis. The BigY Facebook Page reports this manual review could take as long as 12 weeks.

My Block Tree

One way I can tell that things are still changing is by looking at my Block Tree results:

Above I highlighted the private variants. Yesterday I had an average of 10 shared variants. Today I had 12 shared variants. That tells me that things are still happening.

At the same time that I upgraded my BigY from 500 to 700, DNA relative Steve also did a BigY 700 test for the first time. Previously, there were only two people in my branch of the Hartley YDNA tree that had taken the Big Y test. They were Michael and myself. By getting Steve to test, we should be able to get a tie-breaker. By STRs, it seems that I am more closely related to Steve than to Michael, but STRs can be unreliable. The Big Y produces new SNPs which can place us in a different Hartley branch. As the Hartley YDNA branch seems to be fairly old, it is important to find more recent branching. I know that Michael’s genealogy goes back quite far. He has Hartley Quaker ancestors that moved out of the area that my ancestors were living in to find peace from persecution. They moved to Quaker-friendly Pennsylvania. Michael’s ancestor was Edward Hartley. He was born in 1666. He married in 1693 and moved to Pennsylvania probably in the early 1700’s.

Private Variants

Previously, I only had an average 2 private variants between myself and Michael:

The Private Variants are the ones I have and Michael does not have (or that Michael has and I don’t have). This is an average, so it may be two for each, one for one and three for the other or four for one and none for the other.

How Did We Get From 2 Private Variants to 12?

The first answer is that the BigY 700 tests SNPs that were not tested in the BigY 500 test. That means that the new test may be finding new SNPs along the route between Michael, Steve and myself as well as new upstream SNPs. However, I would imagine that the further upstream these SNPs are going back to genetic Adam, the more likely it is that these SNPs have already been discovered by thousands of other BigY testers.

SNP Matching Details

Here are the details of how I do and do not match Michael and Steve:

Looks like a bunch of numbers. From this, I take it that Steve’s test finalized 5 days after mine. If I add up all the Non-Matching Variants and divide by 2, I should get 12. When I add the two, I get 31, so that must be the wrong way to do it.

I put the non-matching and Shared Variants into a spreadsheets:

The only thing that did was show which variants I have that don’t match with both Steve and Michael versus those that don’t match with only Steve or Michael.

FTDNA’s Y-Chromosome Browsing Tool

Under the BigY Results tab, I find this:

Under named variants, I had no results which is confusing because under the BigY matching tab, I had 10 non-shared variants with Michael. Then I had 6 non-named non-shared variants with Michael. With Steve, I had more non-named non-matching variants than named non-matching variants. So I could say that I have no match between my non-matching variants and my Private Variants.

The browser above basically gets at the quality of the SNP. I like to look up positions at YBrowse. Here is what I get when I do that:

According to this list, I have two totally new Private Variants out of 17. Five were previously named by William Hartley – probably when I took my first Big Y. The rest have been named by FTDNA or Full Genomes Corp. The ones that FTDNA and FGC named, they didn’t know where these SNPs appeared on the haplotree. Here is the last SNP I looked up at YBrowse:

When I click on the circled SNP, I get this further information:

Under ycc_haplogroup for the FGC and FTDNA SNP, the comment was ‘unknown’.

My take-away is that I have 17 Private SNPs. There are an average of 12 private SNPs between Michael, Steve, and myself. That would be a total of 36 Private SNPs. That means that Michael and Steve must have a total of 19 Private SNPs between them.

Next, I looked at my non-matching variants and looked those up at YBrowse:

This told me that of my 17 Private Variants, 5 were the same as Non-Matching Variants between me and Steve. I suppose that makes sense because Steve just took a new test and I just upgraded mine.

Now I see my named variants. I must have missed them before or they weren’t there yet:

The list doesn’t say if they are matching or non-matching variants and there are 1775 of them. One issue that I have is with A11130, for example. It shows as non-matching to Michael and Steve, yet it does not show up as a Private Variant for me. Originally when people were naming SNPs, someone thought that A11130 would be a good name for my branch. However, it was later found out that this was a private SNP. That is why people wait for other Big Y matches before they name a branch. That brings up another point. My current SNP name is A11132:

However, A11132 is only representative of the above 7 SNPs. It looks like A11132 was chosen as it was the lowest number in the group.

Alex Williamson’s Big Tree

The Big Tree was used as the model for FTDNA’s Block Tree. Although the Big Tree is slowly being phased out, it still has useful information in it. This is what the Big Tree as my ‘Unique Mutations’:

The BigY2 was from my BigY 500 test where I uploaded additional information.

Here are some notes from the Big Tree Website:

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 good thing about the Big Tree is that it also shows details for Michael. Here are his unique mutations:

Here are some further notes:

The mutations unique to this man are summarized in the table below. Those with a ‘+’ or ‘*’ confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

I don’t know how much further light this sheds on the situation. It appears that both Michael and I have have 5 SNPs marked with a ‘+’. However, our average number of unique SNPs used to be three at FTDNA but this later went down to 2 for some reason. Also note that Michael shows A16717, but with a ** designation. The BigY 700 showed that I had A16717 as a Non-Matching Variant with Michael. That could mean that we are both positive for that, but that Michael didn’t have a good read, so it was rejected on his side. I suppose that these are some of the issues that FTDNA needs to sort out.

Shared Variants

While we are being confused, I’ll add this in. FTDNA shows that I have one Shared Variant with each of my five matches.

I don’t know what this means. However, going to the learning center explains it:

I think this should have said “…the number of known variants…” I probably used to know this. The confusion is that the column before this is Non-Matching Variants and the position number or name of the Variant. I interpreted the Shared Variants to be a uniquely shared variant with the position number. However, this is the number of variants I share. For example, with Steve we have both taken the Big Y 700. So out of 695, 105 variants or SNPs we share 675, 590. I share much less with Michael as he has not upgraded to BigY 700. Here, it would help if FTDNA told you if your match took the old BigY 500 or the new BigY 700. That makes one thing I understand.

Checking My Logic On Non-Shared Variants

According to the FTDNA Learning Center:

I take this to mean that this list does not just include variants or SNPs that I have and my match doesn’t have, but could include variants or SNPs that my match has and I don’t have.

FTDNA – BiGY Facebook Group

This Facebook Group has been helpful. They have a document there called: BiGY-700 I am a Newbie. The last bullet on Page 13 of that document says:

Check your Private/Unnamed Variants, and see if they are found in
your BiGY Matches’ Kits. If so, your Haplogroup will change after a
Manual Review.

Here are my Private Variants:

All I have to do is ask Steve if he has any of these and the ones that match with me should form a new Branch. However, I already know that the Variants in blue will not form a new branch. That is because the SNPs or Variants in blue are already on the list of Non-Matching Variants between Steve and myself. I really need clear instructions like the ones on the BigY Facebook Page because the terminology is so counter-intuitive. Why would I even think of finding a match with my Private Variants list? How are they Private if they match?

News From Steve

Steve wrote back to me with his private variants:

Steve has 19 altogether. The following is actually his first 10 Private Variants:

This is almost like looking at a secret decoder ring.

I put Steve’s Private Variants next to mine and found quite a few matches:

The matches are in gold on my list. The blue Private Variants are ones that are specifically listed in the Non-Matching Variants between Steve and myself. There are 11 Private Variants that match between Steve and me.

Next, I just have to wait for FTDNA’s manual review to see if a new Hartley YDNA Branch is formed.

Summary and Conclusions

  • The purpose of Steve and I doing this BigY test is to see if a new Hartley Branch forms from YDNA.
  • My assumption was that Steve and I are more closely related to each other than to Michael. If Steve and I form a new Hartley Branch and Michael stays in the existing Haplogroup, then that will prove my assumption to be true.
  • YDNA is basically a simple concept. However, the terminology and instructions make things more complicated than they really are. The only part that probably is complicated is the interpretation of the quality of the test results.
  • The FTDNA BigY Facebook site has some good information which counteracts some of FTDNA’s confusing information.

 

 

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