gnomAD gnomAD v3 Genome Coverage Track Settings

Genome Aggregation Database (gnomAD) Genome Sample Coverage v3.0.1

Configure track container: Genome Aggregation Database (gnomAD)

Description

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators at the Broad Institute and collaborating institutions, with the goal of aggregating and harmonizing exome and whole-genome sequencing data from large-scale sequencing projects spanning disease-specific cohorts and population genetics studies. Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. For each variant, gnomAD provides allele frequencies stratified by genetic ancestry group, alongside quality metrics such as depth of coverage and genotype quality scores. The database also supplies sequencing coverage, structural variants, CNVs, and short tandem repeats. Additionally, gnomAD provides non-coding constraint and gene-level constraint metrics — including pLI scores, observed/expected (oe) ratios, and LOEUF values — that quantify intolerance to loss-of-function variation and are widely used to prioritize candidate disease genes. The most current release on hg38 is v4.1, but the older v3 and v2 versions are also available.

The available data tracks are:

gnomAD v4.1 — Shows single nucleotide variants (SNVs) and small insertion/deletion variants of 807,162 individuals, including 730,947 exomes and 76,215 genomes.
gnomAD v3.1.1 — Shows variants from 76,156 whole genomes (and no exomes), all mapped to GRCh38/hg38.
Deprecated: gnomAD v3.1 — Same underlying data as v3.1.1 with older annotations. Do not use; will be removed soon.
gnomAD v3 — Shows variants from 71,702 whole genomes from the v3.0 release.
gnomAD v2 — Shows variants from 125,748 exomes and 15,708 whole genomes, lifted from GRCh37/hg19 to GRCh38/hg38.
gnomAD Mut Constraint — Shows the reduced variation caused by purifying natural selection for 1kbp windows across the genome (based on v3.1.2).
gnomAD Constraint Metrics — Contains per-gene and per-transcript metrics of pathogenicity (LOEUF, pLI, and Z-scores) for v2.1.1, v4, and v4.1.
gnomAD v3 Genome Coverage — Shows various read depth metrics for genome samples from v3.0.1.
gnomAD v4 Exome Coverage — Shows various read depth metrics for exome samples from v4.0.
gnomAD Structural Variants — Shows structural variant calls (variants >=50 nucleotides) from gnomAD v4.1.
gnomAD Rare CNV Variants — Shows rare copy number variants (<1% overall site frequency) from gnomAD v4.1.
gnomAD STR — Shows short tandem repeat genotypes at disease-associated loci from gnomAD v3.1.3.

For questions on the gnomAD data, also see the gnomAD FAQ.

More details on the Variant type(s) can be found on the Sequence Ontology page.

To view the full description, click here.

All tracks in this collection (13)

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	Full Configure	Mean Coverage	gnomAD Mean Genome Sample Coverage v3.0.1	Data format
	Full Configure	Median Coverage	gnomAD Median Genome Sample Coverage v3.0.1	Data format
	Full Configure	Sample % > 1X	gnomAD Percentage of Genome Samples with at least 1X Coverage v3.0.1	Data format
	Full Configure	Sample % > 5X	gnomAD Percentage of Genome Samples with at least 5X Coverage v3.0.1	Data format
	Full Configure	Sample % > 10X	gnomAD Percentage of Genome Samples with at least 10X Coverage v3.0.1	Data format
	Full Configure	Sample % > 15X	gnomAD Percentage of Genome Samples with at least 15X Coverage v3.0.1	Data format
	Full Configure	Sample % > 20X	gnomAD Percentage of Genome Samples with at least 20X Coverage v3.0.1	Data format
	Full Configure	Sample % > 25X	gnomAD Percentage of Genome Samples with at least 25X Coverage v3.0.1	Data format
	Full Configure	Sample % > 30X	gnomAD Percentage of Genome Samples with at least 30X Coverage v3.0.1	Data format
	Full Configure	Sample % > 50X	gnomAD Percentage of Genome Samples with at least 50X Coverage v3.0.1	Data format
	Full Configure	Sample % > 100X	gnomAD Percentage of Genome Samples with at least 100X Coverage v3.0.1	Data format

Version: Release 3.0.1
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

The Genome Aggregation Database (gnomAD) v3 - Genome Coverage track shows how many times regions of the genomes were sequenced. This track includes several subtracks of average coverage metrics and sample percentage of coverage.

There is no gnomAD v4 genome coverage track because the genomes were unchanged from V3. There is no gnomAD v3 exomes track because v3 was a genome-only release.

Display Conventions

The Average Sample Coverage tracks display the mean and median read depth of the samples at each base position. The details page shows calculated sample percentages for the range of sequence within the browser window.

The nX Coverage Percentage tracks display the percentage of samples whose read depth is at least 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, and 100X at each base position. The details page shows calculated sample percentages for the range of sequence within the browser window.

Methods

Coverage was computed using all 71,702 gnomAD v3.01 samples from their gVCFs. The gVCFs were produced using a 3-bin blocking scheme:

No coverage
Reference genotype quality < Q20
Reference genotype quality ≥ Q20

The coverage was binned by quality using the thresholds above and the median coverage value for each of the resulting coverage blocks was used to compute the coverage metrics presented in the browser. Coverage was computed for all callable bases in the genome (all non-N bases, minus telomeres and centromeres).

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory.

The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site.

Credits

Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here.

References

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197

Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194

Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198