SNP Chips vs Whole Genome Sequencing - What Is In Your Raw Data

When a testing service sends you a raw DNA file, it is easy to assume you now hold your entire genome. You almost certainly do not. Most consumer tests use a genotyping chip that reads a curated slice of your DNA - and knowing the difference explains a lot about what your file can and cannot do.

Two very different technologies

• Genotyping arrays (SNP chips) check a fixed, pre-selected list of positions - typically several hundred thousand of them. The chip is designed to read variants that are already known and considered informative.
• Whole genome sequencing (WGS) reads across essentially all of your roughly three billion base pairs, including rare and previously unseen variants.

A consumer raw file is almost always the first kind: a few hundred thousand chosen positions out of billions. That is a small fraction of your genome, deliberately chosen rather than random.

Why chips dominate consumer testing

Arrays are cheap, fast, and reliable. For common-variant ancestry and trait exploration, the pre-selected positions carry most of the useful signal, so a chip delivers a lot of value at a fraction of the cost of sequencing. That trade-off is exactly why the big consumer services use them.

What you give up

The limits matter when you push past common variants:

• Rare variants are mostly invisible. If a position is not on the chip, it is not in your file, no matter how significant it might be for you personally.
• Nothing novel gets discovered. Arrays can only report what they were designed to look for.
• Coverage has gaps. Your file is a sparse sampling, not a continuous read of each chromosome.

Where imputation fits in

To stretch chip data further, services often use imputation - statistically filling in nearby positions that were not directly measured, based on patterns common in reference populations. It is a reasonable way to expand coverage, but imputed values are educated inferences, not direct reads. Your downloadable raw file usually contains the directly genotyped positions rather than the full imputed set.

What this means for your file

None of this makes chip data bad. It makes it specific. Your raw export is a compact, curated set of well-understood positions - excellent for private trait exploration and ancestry signals, and easy to analyze on your own device. It is simply not a complete genome, so treat any single missing variant as expected rather than alarming. For more on how those positions are recorded, see our tour of a raw file line by line and the primer on what SNPs are.

Whatever the source of your file, you can explore it privately with on device DNA analysis or follow our browser based walkthrough - your data never leaves your device.

This article is educational and is not medical advice.