Novel variant question

[Brunetmj]

Are novel variants the same as private SNPs ? If you tested all the novel SNP 's would that bring your SNP line mutations into the present?

[JimKane]

Sometimes, yes. Sometimes, no.

Novel variants are those which have not yet been identified by any research prior to Big Y testing, or were not released publicly like BISDNA's Chromo2 S-series. Since you are in one of the R1b-L21 subclasses, the best way to determine if they are truly novel is to check the R1b-L21 Yahoo forum. Mike, Alex, Chris, and myself all have various distilled versions of the raw results.

If you look here: Big Y Variant Frequency by Haplogroup you can see which variants are occurring under R1b-L21. As I collect Big Y results outside that group, they also appear. If column BF is a 1, then the variant truly is private for now. Those with only 2 may also be private to a given line, but have multiple testers.

Your second question is quite interesting, but I don't have an answer. There seems to be enough SNPs to get you a good deal of the way toward the present certainly. It all depends on what you accept as the mutation rate as to when you wind up though.

[Brunetmj]

Thank you for your responce. I had suspected as much but just wasn't sure. I am close to completeing testing on all my novel snp's.

[John McCoy]

I'm happy to see the Big Y Variant spreadsheet, because it tells me that someone is indeed trying to find a home for the novel variants. However, I have no way of knowing if my own results have in fact been "distilled" into that spreadsheet -- no kit numbers! If it turned out, for example, that my kit wasn't included, I would want a method to contribute my results. When conclusions are based on such an analysis, it is important to know the source of the data, and specifically, what kits are included.

It would be a big step forward if the R-L21 project front page could include links to this spreadsheet and any other useful documents that may exist. I would prefer to see results communicated to the project as a whole, and I think the project web site is the logical place to do that.

[JimKane]

I'm happy to see the Big Y Variant spreadsheet, because it tells me that someone is indeed trying to find a home for the novel variants. However, I have no way of knowing if my own results have in fact been "distilled" into that spreadsheet -- no kit numbers! If it turned out, for example, that my kit wasn't included, I would want a method to contribute my results. When conclusions are based on such an analysis, it is important to know the source of the data, and specifically, what kits are included.

There is another companion which actually breaks down to the source level. Big Y Matrix

Anyone who would like to contribute is free to send a copy of their raw results VCF and BED files to the email address in the matrix version. I do ask if you are outside L21 that you also let me know your major subclade, so that I don't need to hunt it down after the preloading stage.

[John McCoy]

Even better! I will send the files. I can only suppose that even more data would be available for the analysis if the existence of this effort, and others, were listed on the web site of the R-L21 project.

[Brunetmj]

I am just curious if these variant results have been verified elsewhere ?
So far I am showing two of ten variants to differ with independent testing.

[JimKane]

I am just curious if these variant results have been verified elsewhere ?
So far I am showing two of ten variants to differ with independent testing.

I'm not sure how diligent other groups are being with confirming their Big Y tests honestly. The FGC5496 cluster you are a member of actually seems to be doing this the correct way and getting a second lab to verify them all. Outside the group I've not seen a lot of discussion on this though.

[Brunetmj]

Well fortunately , the majority of them seem to be accurate . Thank you for your feedback.