Whitson R-U106 BigY Non-Matching Variants and STRs

The title to this Blog is a bit specialized. There are three Whitson relatives who have taken the BigY test. This group of Whitsons are on the R-U106 general branch of humanity. From there, the Branch has narrowed down to a block of SNPs represented by the name R-FT137411.

In my previous Blog, I started looking at the three Whitson Testers’ Non-Matching Variants. So far:

  • Tom – He didn’t show any private variants. However, his date to common ancestors with Pete and Norton implies that he should have some.
  • Pete – He didn’t show any private variants, but two of his variants which don’t match with Tom and Norton could be Private Variants. The testing for Tom and Norton seemed to show that they didn’t have BY44298 and BY55572. I suggested that these two SNPs may be a new Branch for Pete once Pete’s brother’s BigY test is completed.
  • Norton – He has one Private Variant which he is clearly positive for and Tom and Pete are negative for. This Private Variant is at position 5014418.

Pete and Norton’s Non-Matching Variants

Here is the view from Norton’s perspective:

The non-matching variant between Norton and Tom represents Noton’s Private Variant. The first two named Non-Matching Variants between Norton and Pete were addressed in my previous Blog. That leaves six non-matching variants to look at between Peter and Norton.

BY151409

First, I’ll check Pete’s results:

Pete is showing positive for that SNP. That must mean that Norton is negative for this SNP:

This shows Norton as not derived for BY151409. But it also shows that this SNP is on the Y-Tree. Here are Norton’s test results:

If this SNP is on the Y-Tree, it must not be a private variant. I think that this information is either not helpful or not acurate. I don’t think that BY151409 is on the Y-Tree. Here is what YBrowse shows:

To be complete, I’ll check Tom’s results for this SNP:

FTDNA considers Tom a no-call for this SNP:

Tom only had two good reads:

A third not-so-good read had the mutation as T, when Pete’s mutation was to G, so something is off there. That could mean that this variant could be a Private Variant for Pete also.

BY151410

OK, only 7 variants to go. I will make a summary chart to keep track:

Finishing the Whitson Non-Matching Spreadsheet

It seems that Pete should have as many as 10 Private Variants which seems like a lot. That would be 11 Private Variants divided by three people or about an average of 4. However, it seems like once a variant is named it is not included in the Private Variant category. However, my understanding is that the named Private Variants are not treated the same way as unnamed Private Variants. The SNPs for Pete appear to have been named during Pete’s earlier testing. However, as far as I know, there are no other matches to these SNPs – unless they are in other Haplogroups.

I found this in a R-U106 Forum:

* There is a long, complex, and (mostly) documented description about how the data is extracted from the DNA and ends up in the BAM files, which are then parsed into the VCF+BED files we’ve been requesting for the Warehouse. I won’t go into that here. 
* This data then undergoes some extra processing. Those that match certain quality criteria are extracted and presented as a list of high-quality variants. These high-quality variants are then compared against everyone else in the tree, who is given a positive, negative or null call.
* SNPs where you are positive and others are negative (or vice versa) are used to define your non-matching variants. These are what are listed in your BigY matches.
* Your list of high-quality variants is then subject to a blacklist, removing any SNPs in problematic regions (DYZ19, the centromere and Yq12) and recurrent SNPs found elsewhere in the haplotree. These are listed as your private variants. The blacklist removes regions where complex mutations can lead to mis-mapped regions, missing data or other problems. These complex mutations can then masquerade as one or more SNPs.
Consequently, there may be many reasons why SNPs in your non-matching variants may not appear in either your private variants or your match’s private variants, and vice versa.
So I suppose my question is whether Pete’s non-matching variants include blacklisted SNPs. My sense is that they probably do.

R-U106 Whitson STRs

As suggested by Pete, the private SNPs for the three Whitson testers, do not appear to adequately describe the time to common ancestors. Pete has a common ancestry with Norton at 1835 and with Tom at 1725. Based on that, there should be roughly an average of one private SNP between Norton and Pete and two between Pete and Tom.

It would seem at this point that the STRs show some accuracy in this Whitson Line. Here is the relevant portion of the U106 Whitson STRs:

The third row is the mode of the three testers. The fifth row shows Pete’s results. His results are the same as the mode. In drawing STR trees, the Mode is considered the ancestral value. So that would mean that Pete has had no STR mutations in the 111 series since 1725. I get a tree something like this:

This shows that there are been one STR mutation between Pete and Norton since 1835 and that there have been two STR muations between Pete and Tom since 1725. I suppose that I should have put the 1725 in the red box above.

As this is a combined SNP and STR tree, I can add Norton’s Private Variant:

The confusing part are Pete’s 10 non-matching SNPs. Norton tested negative for these  and Tom had all no-calls. I will wait to see Pete’s brother’s BigY results to see if any of those SNPs come into play.

Summary and Conclusions

  • I think that I’ve taken the U106 Whitson YDNA about as far as it can go with the information I have.
  • I found it somewhat difficult to understand the nuances of non-matching variants and what they are useful for.
  • Previously, I had suggested that two Pete’s non-matching variants may become a new branch. After looking more closely at Pete’s non-matching variants, I am not so sure. I will like to see how Pete’s brother’s BigY test shakes out.
  • I summarized the testing quality for Pete’s non-matching variants in the other two Whitson BigY testers
  • I drew a combined SNP/STR tree for the U106 Whitson branch. Given the time periods Pete gave me to his common ancestors, these STRs seem to fit in better than what we have for Private SNPs right now.
  • I am looking forward to the BigY testing for Peter’s brother.

 

 

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