FTDNA vs Yfull "private" SNP confusion?

[A.Morup]

Hi Mike!

Thanks for your very complete answer.
It was the automated results, so I guess next step is writing Michael Sanger.

Thank you very much!
Anders

[TigerMW]

Hi Mike!

Thanks for your very complete answer.
It was the automated results, so I guess next step is writing Michael Sanger.

Thank you very much!
Anders

Do you have new branching? or do you need a haplogroup label manually updated? These would be the reasons to engage Michael Sager. He's free but his job to update the haplotree and make sure people are on it in the right place.

Evaluating singleton (some say private) SNPs for validity, region stability is not something he does. It should be related to branching to engage him.

If you are just evaluating your singleton SNPs I trust your YFull interpretation is quite adequate. Your to do if there is no new branching is go get some. That's what I meant about recruiting people who are on your matching screen or who you share STR signature patterns with for Big Y testing.

[A.Morup]

Hi Mike!

I have a very close match that I found through Y37 and BigY (and now Y111) and we are working tightly together to locate our common ancestor through the paper trail - Y111 says he must be just around the corner from where we are now (the year 1590 and 1655). Together we have 26 "novel" SNPs according to FTDNA - and a big step under BY3604 (see here at Ytree). I guess that we will see a new haplogroup under BY3604 forming with the next update of the Yfull tree. FTDNA has had our data for over 6 months, but did not update their tree (but that is not the issue here).

We are at distance 4 at Y111 and have now shared the cost of third person (distance 10 at Y111) to take a BigY to elaborate our haplogroup under BY3604.

Besides that, I am now proactively testing distant male cousins SNP by SNP at Yseq to see when my novel SNPs occured since this year ~1600 BigY match - just because it is possible.
But the question is, which SNPs to test, when Yfull and FTDNA does not agree?

My novel SNPs according to FTDNA: 16604xxx, 22271xxx, 22974xxx, 7511xxx
My novel SNPs according to Yfull: 16604xxx, 3882xxx, 7511xxx

22271xxx turned out to be in the DYZ19 zone
3882xxx is homologuos at Yfull and useless according to Yseq - so why does Yfull even list it as an "Acceptable quality" SNP?

Still wondering what happened to 22974xxx at Yfull - they initially rated it "Acceptable quality", but it disappeared as a novel SNP at Yfull, when my close match was processed. However, Yseq has just tested and confirmed it present in a remote cousin (MDKA born 1838).

So - which novel SNPs can I test for between my close BigY match and today - that's the question...

Kind regards
Anders

PS: Gave up writing to Michael Sager - no need to waste his time with private SNPs

[RobertCasey]

A.Morup -

The most economical way to determine stability status of any Y chromosome position is to make "Wish a YSNP" at YSEQ (author of the ISOGG YBrowser). For only $1 each and now a minimum of $10 (new requirement). They will respond by adding all YSNPs into their ordering system (FTDNA will not do this) AND they will also reject all YSNPs in questionable areas with a very brief description. YSEQ is the strictest of all of the organizations for avoiding any possible inconsistency of testing in the future.

But YSNPs in unstable areas can be extremely useful as well. Under L226, we originally included eight branches on our haplotree in unstable areas. After 50 NGS tests under L226, we had to remove two branches that had results inconsistent with the haplotree (some are still on the FTDNA haplotree and BigTree haplotree). Three of the remaining six branches are very significant major branches. So if you just discard YSNPs in unstable areas, you are going to have to do a lot more testing to get the same results. From a genealogist point of view, you would be discarding all records on deeds since they do not involve relationships in most cases - but sometimes are gold mines for "Deed of Gift" to children that would be missed.

Other the other hand, YSNPs in unstable areas are a real pain to test. Some can only be tested by NGS testing. YSEQ will not allow these private YSNPs to be tested, so you lose that important source of testing. FTDNA's Mass Array technology (SNP packs) including a good portion of these YSNPs which have been very useful. Even Sanger Sequencing (individual YSNP testing) can not read several classes of these YSNPs in unstable areas. Under L226, our genetic bottlenecks reside under three major branches based on YSNPs in unstable areas. BY4100, Z17669 and DC40 have a whopping 68 private YSNPs stuck under these three branches (which have consistent testing results over 50 NGS tests and 50 more SNP pack tests).

If we removed these branches, they would combine with other branches that already home to even more private YSNPs. BY4100 and DC40 are two branches in unstable areas that include 10 % of L226 testers at 67 markers. If they were not used, both would roll up to FGC5628 which covers over 50 % of L226 (both in known branches and total testers). The third major branch in an unstable ares is Z17669 which includes 80 % of L226. Without Z17669, our oldest first branch, DC69, would get lumped in together with starburst of six other branches. So these branches in unstable areas are worth testing - even if they could become inconsistent later and even if testing is much more of a challenge across technologies.

[vettor]

As noted to me by Yfull team recently...............my private SNP will become a non-private marker once a person who is not a family member is found. Once this happens , your once private marker will be a public marker and added to the yfull tree.

[asquecco]

Hi,
about 22974xxx at Yfull, if you Browse raw data for that position can you see the row "Known SNPs at this position:" ?
Adriano

[A.Morup]

Hi,
about 22974xxx at Yfull, if you Browse raw data for that position can you see the row "Known SNPs at this position:" ?
Adriano

Yes - "YFC235673", but no "Known SNPs at this position" for 16604xxx and 7511xxx.
So not private anyway?

Thanks
Anders

[asquecco]

As far as I know YFC = YFull Candidate SNP. That's why it disappeared from the Novel SNPs list.
But YFC SNPs are not yet listed in "Hg and SNPs - Known SNPs" TAB so at the moment it seems we have an issue if we want to list YFC SNPs + Novel SNPs for a kit.
Adriano