Why Y-DNA and Mitochondrial DNA Are Missing From MyHeritage Whole-Genome Data

The short answer: missing Y-DNA and mitochondrial DNA is almost always a file format or analysis limit, not a failed sample and not a reason to distrust the autosomal data. MyHeritage does not sell whole-genome sequencing; if you have a whole-genome CRAM or VCF, it came from another lab. A standard MyHeritage DNA export is a genotyping array, not whole-genome sequencing; it measures roughly 700,000 mostly autosomal markers. A true whole-genome CRAM or VCF can also omit Y-DNA and mtDNA because many pipelines keep only the autosomes and X.

Why is my MyHeritage whole-genome file missing Y-DNA and mitochondrial DNA?

Start with the file type. The raw CSV you download has about 700,000 rows. Almost all of those rows are on chromosomes 1 through 22, with a smaller number on X. Y-DNA and mitochondrial DNA are only sparsely represented on that array, if at all. So a MyHeritage raw file can look whole-genome to some tools but it is not whole-genome coverage.

Now suppose you actually have a whole-genome file, a CRAM or VCF from a sequencing provider. If you are biologically male, the sequencer likely captured reads from chromosome Y; in everyone it likely captured mitochondrial reads. But a VCF is not raw reads. It is a list of sites where the pipeline found variation against the reference. Many pipelines exclude chrY and chrM by default. The reasons are practical. Chromosome Y is haploid in males and absent in females, so a standard diploid caller can call it badly. Mitochondrial DNA exists in many copies per cell, so it needs a different model for heteroplasmy. Some labs simply remove those contigs from the export rather than report them badly.

Missing Y-DNA and mtDNA is a file or analysis choice, not a failed sample and not a reason to distrust autosomal data.

What a whole-genome CRAM can and cannot tell you

A CRAM file is compressed aligned reads. It can tell you whether sequence reads from chrY and chrM are present, but it does not give you a neat haplogroup by itself. If reads mapped to those contigs, the data were captured. You or an analyst would still need to call variants with chrY and chrM included, set the ploidy correctly, and compare the calls against a haplogroup reference.

The mitochondrial genome is 16,569 base pairs. The Y chromosome is around 57 million base pairs, with large repetitive stretches that are hard to map. A genotyping array probes a fixed set of roughly 700,000 positions. For deep Y-DNA or mtDNA lineage assignment, you need dense coverage of specific branch markers, not a few scattered SNPs.

What it looks like when you open the file

• In a MyHeritage raw CSV, the chromosome column is the quickest check. Most rows are 1 to 22 and X. Filter for MT or Y and you will usually see very few or no rows.
• In a whole-genome VCF, look at the header lines that start with ##contig. If there is no ##contig for chrY or chrM, the file was filtered after alignment.
• In a CRAM loaded into IGV, zoom to chrM. You will often see very high coverage in a normal sample. In a male, zoom to chrY and you will see about half the depth of the autosomes. In a female, chrY coverage is near zero.

That pattern is the useful distinction. High chrM coverage or half-depth chrY coverage means the sequencer captured the molecules. The absence in a VCF came later, in analysis.

When a separate Y-DNA or mtDNA test is worth ordering

Order one if you want deep paternal or maternal line history and your current file has no chrY or chrM calls you can use. A dedicated Y-DNA test follows the male line. A full mitochondrial sequence follows the maternal line. Autosomal DNA is bad at deep lineage because it recombines every generation. Y and mtDNA pass down almost unchanged. If you have a whole-genome CRAM with reads on chrY or chrM, you may not need to give a new sample. You may only need reanalysis from the same file.

The mistake people make with missing Y-DNA and mtDNA

People assume the sample failed, the lab made an error, or the autosomal results are now suspect. None of that follows. Autosomal calls are independent of mtDNA and Y. A sample can produce excellent autosomal data and still have a VCF that omits chrY and chrM. The opposite also happens. Some files include a few Y or mtDNA positions that look informative but are too few to assign a haplogroup. Do not read deep ancestry into five markers.

HealthOS has a free DNA tool that reads a MyHeritage CSV or a whole-genome VCF in your browser. It reports traits, medication response, carrier-relevant findings and an optional ancestry breakdown. If your file has usable Y or mtDNA markers, the lineage section reads the maternal and paternal haplogroups on your device. Run it at HealthOS DNA analysis.