Raw Data and Y-DNA results
I just wanted to share something that happened with me, my data, and Ancestry recently. Obviously, this is for you men out there, since it's concerning Y-DNA.
So I learned about MorleyDNA from a comment here. MorleyDNA is a long-established, well-respected tool in the genetic genealogy community. It's run by Chris Morley, an individual hobbyist researcher, and has been operating since 2013. It's routinely recommended on WikiTree, Anthrogenica, the FamilyTreeDNA forums, biostars, and by independent genetic genealogy bloggers, from what I can find. I did some research because I was iffy about uploading my raw DNA data file to some site, but once you upload, it just extracts the Y-DNA and reads that, it doesn't read the whole file. In other words, only ~500–2,000 Y-chromosome SNPs get sent to the server, not your whole file.
Anyway, so I uploaded my raw data file and it came back with zero results. I thought this was odd, considering I'm male and this is supposed to be my entire DNA genome in a .txt file. So I scrolled to the bottom of the file and it only went up to 23 chromosomes, my AncestryDNA raw data download was missing chromosomes 24 (Y), 25 (mtDNA), and 26 (PAR) entirely. So, admittedly, I did some back and forth with ClaudeAI about the issue, and it recommended I reach out to AncestryDNA support, so I did (*I got help from Claude with phrasing and to make sure I got all of the information across that was necessary to get to the bottom of this*).
I got into a chat and messaged the following:
>My raw DNA data download is missing chromosomes 24, 25, and 26 entirely. I'm a biological male and would expect Y-chromosome and mitochondrial data to be present.
Their AI chatbot responded:
>Because we only offer an autosomal DNA test 🧬, your raw DNA download won’t include Y‑DNA or mitochondrial (mtDNA) results. Also, chromosomes labeled 24, 25, and 26 are often just a labeling difference in whatever software you’re using to view/import the file (some tools refer to X and Y as 23 and 24).
Claude recommended that I push for a human representative. I did so, explaining that:
>I'm a biological male, but my AncestryDNA raw data download is missing chromosomes 24 (Y), 25 (mtDNA), and 26 (PAR) entirely. My file only contains chromosomes 1–23. I've confirmed this by opening the .txt file inside the .zip and scrolling to the end — chromosome 23 is the highest value present.
>I noticed this when trying to use a third-party Y-DNA haplogroup prediction tool, which returned zero recognized Y-SNPs. These chromosomes should normally be present in AncestryDNA raw data for male testers.
>Could you please check:
- What biological sex was determined for my sample during processing?
- Were there any quality control flags or issues with my sample?
- Can my sample be re-run, or can I receive a replacement kit?
>Thank you.
The human representative I got in touch with gave me the following response:
>AncestryDNA only offers autosomal DNA testing, which provides a comprehensive overview of ancestral origins and genetic relatives. It does not provide Y-DNA testing, which is necessary for males to trace their patrilineal ancestry through the Y-chromosome. Consequently, the absence of chromosomes 24 (Y), 25 (mtDNA), and 26 (PAR) in your raw data file is expected, as AncestryDNA does not include Y-chromosome data in its results. This limitation explains why your Y-DNA haplogroup prediction tool returned zero recognized Y-SNPs.
So I could have taken this as it was and been done with it, but I plugged this response into Claude and it immediately called this out as false. AncestryDNA has historically included chromosomes 24 (Y), 25 (mtDNA), and 26 (PAR) in their raw data reporting, even though they don't report it to consumers. So I doubled down and asked the rep to escalate this to a DNA specialist or technical support team who can actually review my sample's processing records to ensure my biological sex was coded as male and whether any quality control issues were flagged for my sample. They agreed to escalate this by creating an error report.
I then received an email from Ancestry with the following information:
>Thank you for your response regarding the technical composition of our raw data files. You are correct that our files historically utilize custom labels for sex chromosomes and mitochondrial data, mapping Chromosome 24 to the Y-Chromosome, Chromosome 25 to the Pseudoautosomal Region, and Chromosome 26 to Mitochondrial DNA.
>We have escalated your inquiry to our DNA technical support specialists to review your specific sample processing records. Our team will verify the biological sex determined during lab processing and check for any quality control flags that may have affected your data.
So fellas, the moral of the story is, if you're at some point interested in your Y-DNA at all, and you don't get it in your raw data, escalate the situation, because this data should be included if you download it!