Frazer YDNA Loose Ends and Private Variants

In my previous Blog, I was caught a little off guard as I didn’t know that Rodney had tested for the BigY 700. However, that was good news as now we have a BigY 700 in both the James and Archiald Lines of the Frazer YDNA Tree. One confusing thing about FTDNA is that it is difficult to know when your BigY test has been completed. Here is Rodney’s order history:

This seems to indicate that his BigY was completed on January 14. However there are still more tests ordered by FTDNA. Another way to check is if Rodney’s Private Variants match up with the average Private Variants shown on the Block Tree. [Note: Later in the Blog I show that is not a good way to see if your BigY has completed.]

Here are Rodney’s Private Variants:

Rodney now has 7 Private Variants. These are described by their position numbers to distinguish them from SNP which need to have a match with someone. To get the average number of Private Variants for the James Frazer Line, we need to know the number of Jonathan’s Private Variants:

Jonathan has two. This averages out to 4.5. The Block tree shows an average of 4:

4 is close to 4.5, so I would say that the BigY analysis is complete – except for the Backbone Tests. The number of Average Private Variants went up from 2 to four probably on January 11th when the backbone test was ordered or on on January 14th when FTDNA shows the BigY was completed.

Rick’s Results

Rick shows that his BigY completed in December:

However, Rick has nine Private Variants:

Paul who is on Rick’s Branch has one Private Variant.

That is a total of 10 for Rick and Paul’s Frazer Branch for an average of five Private Variants. The Rick and Paul Branch of the Block Tree shows an average of three Private Variants. That means that FTDNA’s manual review must not be completed yet.

The James Line Private Variants

These should be the variants that have formed since Rodney’s and Jonathan’s common ancestor.

That common ancestor was Thomas Henry Frazer. Thomas Henry Frazer had, for sure, these two SNPs – Y151390 and FT421607:

I say, for sure, but the backbone tests seem to be confirming these. The point is that Rodney and Jonathan’s Private SNPs formed after Thomas Henry Frazer in 1836. By the way, I made a mistake in dating the Block Tree in a previous Blog, so I’l correct that here:

The slightly confusing part is that the 1836 is higher on the tree than the 1804. I think that could change as the average number of Private Variants right now appears to be 5 between Paul and Rick under the R-Y85652 part of the Tree. Say that some of the testers were born around 1950. That would mean that this Tree represents 750 years of Frazer YDNA history.

Jonathan’s Private Variants

Here is Martin’s take on Rick’s initial results. Martin is the FTNDA administor for the portion of the R1a YDNA Tree that our Frazers are on. These have since changed since Rodney’s BigY 700 upgrade came in.

This shows Rick with a BigY-700, but doesn’t show Rodney in that category yet. I mention above, that Rodney has 7 Private Variants. The BigY 700 is more comprehensive and finds more variants. Before Rodney’s BigY 700 results came in, he only had one Private Variant. Jonathan has two Private Variants. They are the last two in the yellow box aove.

Jonathan’s first formerly Private SNP became part of the new James Line Haplogroup:

I don’t see BY84935 on the Block Tree, so if it isn’t there and isn’t on Jonathan’s Private Variant list, where did it go?

Here are Jonathan’t test results:

The mutation should be G to A, but Jonathan shows at least two reads that are G to T.

Let’s see how Rodney tested for this. This is now a named SNP, so no longer a Private Variant for Jonathan. I don’t see Rodney having BY84935:

Based on these two test results, this should still be a Private SNP for Jonathan.

Rick and Paul Have a ? for BY84935

Rick is sometimes positive for this SNP and sometimes not. Also, he seems to have a lot of similar results in this region of the Y Chromosome. Now I see why they took away this Private Variant from Jonathan.

Let’s check out Paul’s results:

Very similar to Rick’s results:

Based on these results, I’m a bit surprised that Jonathan ever had a Private Variant at this position. For Jonathan’s other two Private Variants, I will assume that they are correct. The bottom line is that Jonathan has two Private Variants. These are:

  • 11718822 and
  • 11720223

These had to have formed in Jonathan’s line in either Edward, Walter, or Jonathan:

In a sense, these Private Variants are not important from a genealogical point of view. Jonathan already knew he was a second cousin to Rodney. However, if anyone else ever tests positive for these Variants in the future, it will show that they are from this same Edward Fitzgerald Frazer Line.

Rodney’s Seven Private Variants

There is another use of Private Variants. These can be used to date the common ancestor between two people. A number between 83 and 144 years is generally used. However, that time-frame does not work well in the case of Rodney and Jonathan. Their ancestor is believed to be Thomas Henry Frazer born 1836. Even if we take that date from 2021, that is 185 years ago. That means that, at most, there should have been an average of three private variants between Jonathan and Rodney where there are 4 (and actually 4.5). That means that these Variants were forming about every 40 years or about twice as fast as would be expected, on average.

Here are Jonathan and Rodney’s average of 4 Private Variants:

Rodney’s Private Variant at Position # 11830989

I don’t want to go through each of Rodney’s Private Variants, but I will at least look at one:

I don’t think that FTDNA shows test results in the browser for Private Variants if you are not positive for them. Here is Jonathan’s downloaded results for this position:

It looks like Jonathan’s results were less than conclusive.

Next, I’ll look at Paul’s results:

Paul was not tested at that position.

Let’s see what Rick has. I need to download his ‘csv’ file. I would expect that Rick would have good results as he has tested for the BigY700:

Here is a surprise. This shows that Rick has this Private Variant. That means that it can no longer be Private. That is good because it means that Rodney has one less Private Variant. I don’t know why FTDNA didn’t pick this up:

That means that this should be a new SNP included in the umbrella SNP group of Frazer. At YBrowse Position # 11830989 is FT420438:

The good news is that this will take away one of Rick’s Private Variants as he has too many already.

Rodney’s Private Variant at Position # 5987829

I did a comparison of Rodney’s and Rick’s Private Variants and found one more match:

This brings up another reason that Private Variants are important. If they match with someone else’s Private Variant, they form a new SNP. Usually FTDNA will catch that. In this case, they are still in the middle of some of their reviews and have ordered backbone tests for Rodney and Jonathan. It is possible that FTDNA is not sure where to put these new SNPs. This seems to indicate that they are Frazer SNPs, but perhaps they go back even further?

Here is what YBrowse shows:

These two SNPs are interesting as YBrowse shows that they are from an unknown Haplogroup. That seems to support my theory that FTDNA doesn’t know where these SNPs belong. Here are Rodney’s test results for the position:

Here are Rick’s results:

If Rodney and Rick are positive at this Position, then Paul and Jonathan should also be positive.

Paul’s results above were inconclusive.

How about Jonathan’s?

Jonathan’s test results were also inconclusive.

FT420438 and FT420010 Frazer SNPs?

If it was up to me, I would add these two SNPs to this area:

That means that there would be 8 SNPs in this area instead of the current six. So far, everyone how has tested for these SNPs have been Frazers. However, the six or eight SNPs represent four or five hundred years of history. It would be great to fill in some of the blanks for this time period. It may be that FTDNA hasn’t finished their review or are awaiting the results of the two backbone tests they are doing.

Changes to Frazer Testers’ Private Variants

The other change that should be happening is that Rick and Paul’s Average Private variants under R-Y85652 should be going up. They show 3 currently. Rick has 9 but two of these are shared with Rodney. Rick should have 7 Private Variants and Paul has one Private Variant. That should result in an average of four Private Variants under the Archibald Frazer LIne of R-Y85652.

Rodney currently has 7 Private Variants, but two of those are shared with Rick. That should results in 5 Private Variants for Rodney. Jonathan has two Private Variants. If FTDNA rounds down, that will result in an average of 3 Private Variants for the James Line Branch under R-Y151390.

Further, I note this under FTDNA:

This says it could be that the two matches I found between Rodney and Rick could be there because they haven’t properly been properly validated yet. Hence the backbone test which is in process.

Summary and Conclusions

  • I started out trying to figure out if Rodney and Rick’s BigY reviews were done or not.
  • I thought that perhaps Rodney’s review was done because the Block tree average number of Private Variants matched with his and Jonathan’s Private Variants.
  • Then, when I started comparing Rodney and Rick’s Private Variants, I saw that they had two in common. That means that if Rodney’s review was over, there was still two SNPs to be assigned to the Frazer Block Tree.
  • I guessed that perhaps FTDNA had trouble placing these new SNPs and that is why they ordered the Backbone tests for Rodney and Jonathan
  • I had thought that if your Private Variants matched with what the average Private Variants were on the Block Tree, then that meant that your BigY manual review was over. But then I found something at FTDNA that said that may not be true.
  • I had thought that the Backbone tests ordered for Rodney and Jonathan were to confirm their new Haplogroup of R-Y151390. Now it appears more likely that the Backbone test is for the two matching Private Variants that Rodney and Rick have with each other.
  • It could be a month or more before the dust settles for Rick’s new BigY 700 test and Rodney’s upgrade from BigY 500 to BigY 700. By then, we will probably have the results from the new Frazier/Frasher BigY 700 test which has been delayed.

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