What is low-pass whole-genome sequencing?

It reads DNA from across the whole genome at low coverage, often around one read per position, and fills in the gaps by imputation using a reference panel.

What does 1× coverage mean?

It means each position in the genome is covered by about one sequencing read, on average. Some positions get more reads and some get none, which is why low-pass data is paired with imputation.

Is low-pass sequencing better than a SNP chip?

Each has trade-offs. A chip reads a fixed set of markers with high confidence; low-pass sequencing reads far more positions with lower confidence each, and relies on imputation and a good reference panel. A 2022 dog study described low-pass sequencing with imputation as a low-cost alternative to chips.

Is low-pass sequencing the same as whole-genome sequencing?

It's a kind of whole-genome sequencing, because the reads come from across the whole genome. The difference is depth: high-coverage genomes are read many times over, while low-pass sequencing reads each position about once.

Glossary5 min read· October 21, 2026

Low-Pass Whole-Genome Sequencing, Explained

Low-pass whole-genome sequencing reads DNA from across the whole genome, but thinly, then fills the gaps by imputation. Here's how it works, what coverage means, how it compares with SNP chips, and its limits.

By PuppyGenes · How we research and write our guides

Low-pass whole-genome sequencing reads DNA from across a dog's whole genome, but thinly: on average, each position is covered by about one read, and some by none. Because so many positions are read once or not at all, the missing and uncertain genotypes are filled in by genotype imputation, using a reference panel of well-characterized dogs.

The short version

Whole genome, thinly: reads come from across the genome, at low coverage.
Coverage is how many reads overlap a position on average; low-pass is often around 1×.
Imputation fills the gaps, using a reference panel.
Versus SNP chips: a chip reads a fixed set of markers chosen in advance; low-pass sequencing reads millions of positions with lower confidence each.
The trade-off: it's a low-cost approach, but it relies on imputation and a good reference panel.

What coverage means

Sequencing machines read DNA in short fragments, which are lined up against a reference genome. Coverage, or depth, is how many fragments overlap a given position on average. Research genomes are often read many times over: the high-coverage dog genomes in a 2022 study were read more than 15 times over. Low-pass sequencing reads each position about once, so any single position may be missed or read with low confidence.

	High-coverage sequencing	Low-pass sequencing	SNP chip
What it reads	Nearly every position, many times	Positions across the genome, about once each	A fixed set of chosen SNPs
Main trade-off	Costs more	Relies on imputation	Limited to the SNPs chosen in advance

A simplified comparison of the three approaches.

How it compares with SNP chips

A SNP chip, or genotyping array, reads a fixed set of SNPs with high confidence. As the 2022 study noted, chips are ultimately limited by the SNPs chosen when they were designed. Low-pass sequencing takes the opposite approach: instead of reading chosen positions confidently, it combines information from millions of randomly sampled, lower-confidence readings and relies on imputation to turn them into genotypes.

How well it works

The 2022 study thinned 97 high-coverage dog genomes from 51 breeds to about 1× to simulate low-pass sequencing, then imputed them using a reference panel of 676 dogs. After quality filtering, which kept about 80% of the 14 million imputed positions, the imputation error rate fell from 3.0% to 1.5%. Our guide to genotype imputation explains those results.

What this means for a DNA report

Whatever technology a test uses, its results depend on the evidence it reads and the reference data it compares with. The PuppyGenes report combines sequencing evidence with reference-based predictions, and an inferred result is not a definitive direct reading of every genetic position. Our science page explains what each section can and can't tell you, and our guide to reference panels explains why the comparison dogs matter.

Frequently asked questions

What is low-pass whole-genome sequencing?: It reads DNA from across the whole genome at low coverage, often around one read per position, and fills in the gaps by imputation using a reference panel.
What does 1× coverage mean?: It means each position in the genome is covered by about one sequencing read, on average. Some positions get more reads and some get none, which is why low-pass data is paired with imputation.
Is low-pass sequencing better than a SNP chip?: Each has trade-offs. A chip reads a fixed set of markers with high confidence; low-pass sequencing reads far more positions with lower confidence each, and relies on imputation and a good reference panel. A 2022 dog study described low-pass sequencing with imputation as a low-cost alternative to chips.
Is low-pass sequencing the same as whole-genome sequencing?: It's a kind of whole-genome sequencing, because the reads come from across the whole genome. The difference is depth: high-coverage genomes are read many times over, while low-pass sequencing reads each position about once.

From general to personal

See how this applies to your dog specifically.

Our at-home Complete Dog DNA Test adds your dog's own results to these tips across six report sections: breed ancestry, coat colour, physical appearance, temperament and size predictions, genetic diversity and oral microbiome. The report does not include genetic disease or health screening.

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