[genome-announce] gnomAD v4 Exome and v3 Genome coverage tracks for hg38

[Jairo Navarro Gonzalez]

Hello everyone,

We are pleased to announce the release of two new coverage tracks from the Genome Aggregation Database (gnomAD) on the human GRCh38/hg38 assembly. These tracks are part of the Genome Aggregation Database (gnomAD) track collection.

The gnomAD v4 Exome Coverage track displays per-base sequencing coverage statistics derived from the gnomAD v4.0 exome callset. Coverage was computed across all gnomAD v4 exome samples using gVCFs produced with a 3-bin blocking scheme based on reference genotype quality (< Q20 and ≥ Q20). Note that there is no gnomAD v4 genome coverage track because the genome samples have not changed since v3. The track contains the following subtracks:

• Mean Coverage – mean read depth across exome samples at each base position
• Median Coverage – median read depth across exome samples at each base position
• Sample % > 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, 100X – the percentage of exome samples with read depth at or above the indicated coverage threshold at each base position

The gnomAD v3 Genome Coverage track displays equivalent per-base coverage statistics computed from 71,702 gnomAD v3.0.1 whole-genome samples, using gVCFs and the same 3-bin blocking scheme. Note that there is no gnomAD v3 exome coverage track because gnomAD v3 was a genome-only release. The track contains the following subtracks:

• Mean Coverage – mean read depth across genome samples at each base position
• Median Coverage – median read depth across genome samples at each base position
• Sample % > 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, 100X – the percentage of genome samples with read depth at or above the indicated coverage threshold at each base position

For both tracks, clicking a feature opens a details page showing calculated sample coverage percentages across the sequence range visible in the browser window. Coverage data files in bigWig format are available from our download server in the coverage/ subdirectory, and data can also be explored interactively using the Table Browser or Data Integrator. Raw data are also available directly from the gnomAD downloads page.

We would like to thank the Genome Aggregation Database Consortium for making the data public. We would also like to thank Max Haeussler and Jairo Navarro Gonzalez for creating and releasing the UCSC Genome Browser tracks.

Jairo Navarro 
UCSC Genome Browser
UC Santa Cruz Genomics Institute
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