Tweet
This question is mostly for males who have done the Family Finder (autosomal) test since around 2020 (even though as early as 2019 might also fall in this category). I've noticed lots of values where there's a no-call paired with an allele such as -T, -C, or -A in my X-DNA raw data. Which is apparently giving me a relatively high number of "heterozygous" values (as high as 6 %!). So, I was wondering if any other male who has recently done the autosomal test here gotten similar results in the X chromosome data.
-
-
I had a lot of DNA testing done for myself and various family members, but all between 2012 and late 2016-early 2017. I haven't had anyone whose kit I manage do any tests since then. I did check the raw data file for the last person I tested, a male who had the Family Finder test done with results received in Feb. 2017. I had downloaded his raw data in 2017 and for some reason again in 2019, and checked that 2019 file (even though both are probably the same). He had some no calls, but none that showed "-A" or similar. All were "--" instead. Everything else was AA, CC, GG, or TT. I checked one older kit for a male, whose Family Finder results were from a transfer from 23andMe, in 2012 or 2013. The download was from 2021, but for the X alleles it only had one letter ("A" etc.), or "-" for no calls. So both of those are apparently not recent enough and of no use to you, since the later downloads didn't change anything (as we should expect; FTDNA to my knowledge has not rescanned or reformatted results for everyone who tested earlier, to update raw data!).
The Help Center page for "Downloading Family Finder Data" shows near the bottom that
The three heterozygous examples they give are DI, CT or TC, and AG or GA. The hyphen "-" allele value means "no call," and the meaning they give for it is*For men, the X-chromosome raw data file shows doubled values. . . as placeholders even though in reality they only have one X chromosome.
It is weird that you have some -T, -C, -A results in your data. I'm not sure if that's technically heterozygous or something else. You may want to click on the "Customer Support" link at the top right of the forum pages, and ask what it means. You can do a chat, call them, or create a customer support ticket. If you create a ticket, they send a confirmation email and then usually a reply in a couple of days.The results were not clear for this SNP. A small percentage of results like this are expected from microarray chips. -
These Y-DNA results are typical and caused by what is known at the psuedo-autosomal region (PAR) on the Y chromosome. It is about 2 million bases that is identical to the X chromosome so you get a lot of apparently heterozygous positions on chrY. I wrote about this in a somewhat technical article that can be found here: https://www.biorxiv.org/content/10.1101/352732v1.full Most DNA analysis companies treat the Y chromosome as a single entity with the PAR SNPs often heterozygous. Ancestry treats this region as a separate chromosome (chr24) with the Y unique region as chr25. While there should be no heterozygous SNPs on "chr25", there are some and these are due primarily to sequences on other chromosomes that are similar over a short region. At least that was the case when my DNA was tested several years ago. If QC is good, they should have been eliminated from later versions of the chip.Comment
-
Thanks for your answer, but we're not talking about Y-DNA raw data here but X-DNA raw data. Not the same thing at all.Originally posted by thompsonjfent View PostComment
-
Yes and no. I agree that X and Y are different but the point is that there is a 2 million base pair segment that is the same sequence on X and Y. You end up with "heterozygous" SNPs on either X or Y, depending on where you assign the SNPs. So, males will have a significant number of heterozygous calls and they could land on X or on Y, depending on how the company assigns them. When I had my tests done, both Ancestry and MyHeritage placed them all on chrY while 23andMe put them on chrX. Based on your results with FamilyFinder, they must also put them on chrX. Neither placement is wrong as they really are on both X and Y and will sometimes appear heterozygous in either males or females. This region has unique properties which you can read about here: https://www.nature.com/articles/ejhg200863 This is one of the many subtleties of genetics that are not generally discussed.Comment
-
The Nature article linked by thompsonjfent discusses the PAR (pseudoautosomal regions). There are also a couple of threads in the FTDNA forums where this has been discussed in recent (and not-so-recent) years:- Could an X-match be a Y-Match? (2018-2019)
- X matches (2019) PAR is discussed starting with my post, which is linked, and afterward on that page.
- Pseudoautosomal regions (2014, so may not apply to what is included in testing and raw data nowadays. But there are several knowledgeable people who posted in that thread, who don't seem to post in the FTDNA forums anymore)
Comment
Comment