AncestryDNA vs 23andMe Raw Data: What's Different?
Both AncestryDNA and 23andMe let you download your raw DNA file. It’s a text file containing hundreds of thousands of your genetic variants. On the surface, these files look similar. Open them up, though, and the differences become clear pretty quickly.
This guide breaks down what makes each format unique, and why those differences matter less than you might think.
What both files have in common
At their core, both files contain the same type of information:
- SNP identifiers (rsIDs): unique catalog numbers for each genetic position
- Chromosome numbers: which of your 23 chromosome pairs the variant sits on
- Positions: the exact location on that chromosome
- Your genotype: the two letters (alleles) you inherited, one from each parent
Both files are plain text, tab-delimited, and use the GRCh37 (hg19) human reference genome for position coordinates. Both start with comment lines (prefixed with #) followed by a header row, then the data.
How the file formats differ
Despite containing the same type of data, the two services package it differently.
23andMe format: 4 columns
23andMe uses four tab-separated columns:
# rsid chromosome position genotype
rs3094315 1 742429 AG
rs12124819 1 766409 AA
rs11240777 1 788822 --The genotype is a single field with both alleles concatenated together. AG means you inherited an A from one parent and a G from the other. A -- entry means the SNP couldn’t be read (a “no-call”).
Chromosomes are labeled directly: 1 through 22, plus X, Y, and MT (mitochondrial).
AncestryDNA format: 5 columns
AncestryDNA splits the genotype into two separate columns:
rsid chromosome position allele1 allele2
rs4477212 1 82154 T T
rs3094315 1 742429 A G
rs7419119 1 761147 0 0Each allele gets its own column rather than being combined into one string. A 0 in either allele column indicates a no-call.
AncestryDNA also uses numeric codes for non-autosomal chromosomes: 23 for X, 24 for Y, 25 for the pseudoautosomal region (shared between X and Y), and 26 for mitochondrial DNA.
SNP counts: how many variants each file contains
Both services use genotyping chips (microarrays) made by Illumina, but the exact chip versions and SNP selections differ:
| Feature | 23andMe (v5 chip) | AncestryDNA (v2 chip) |
|---|---|---|
| Total SNPs | ~640,000 | ~664,000 |
| Genotype format | Combined (AG) | Split (A / G) |
| No-call marker | -- | 0 |
| Chromosome labels | X, Y, MT | 23, 24, 25, 26 |
| Columns | 4 | 5 |
| File type | .txt (zipped) | .txt (zipped) |
| Reference genome | GRCh37 | GRCh37 |
The SNP counts are close but not identical. Each service picks a slightly different set of genetic positions to genotype, based on their research partnerships and product focus. AncestryDNA leans toward ancestry-informative markers, while 23andMe includes more health-relevant variants.
That said, there’s significant overlap. Both chips are built on Illumina’s platform, and most commonly studied health and ancestry SNPs appear in both files.
Does the format difference affect health insights?
For most practical purposes, no. The format differences are cosmetic: different packaging for the same underlying data type.
Any service that accepts raw DNA uploads handles both formats. The conversion is straightforward. Parsing 23andMe’s combined genotype (AG) into separate alleles (A and G) is trivial, and remapping chromosome labels (23 to X) is a simple lookup.
What matters more than format is which SNPs are included. If a specific variant you care about (say, rs1801133, the well-studied MTHFR C677T variant) is genotyped by your testing service, it’ll appear in your raw file regardless of which company you used. Both services include this particular variant, along with most other commonly researched SNPs.
The real limitation of both services is that genotyping chips only read around 600,000 to 700,000 positions out of your genome’s 6+ billion base pairs. Whole genome sequencing (WGS) services read far more data, but at a higher price point and with a different file format entirely.
What you can do with either file
Your raw DNA file, whether from AncestryDNA or 23andMe, is yours to download and use. Both services let you export it from your account settings.
Once you have it, you can upload it to third-party analysis services that cross-reference your variants against published genetic research. This is where the real value emerges: moving beyond the ancestry pie chart into areas like nutritional genomics, supplement response, exercise tendencies, and more.
SoDNAscan accepts both AncestryDNA and 23andMe raw data files. The system automatically detects your format, normalizes the data, and matches your variants against 256 carefully selected SNPs across 10 biological systems. The output is a personalized health book with confidence-scored insights, where each finding is rated by the strength of the underlying research.
So which raw file is “better”?
Neither. Both give you access to hundreds of thousands of genetic variants, and both can be analyzed for wellness insights well beyond what either company’s standard reports offer.
The most important step is downloading your file. Whichever service you used, your raw data is sitting there right now. And it contains far more information than any ancestry report has shown you.