gnomAD Coverage Super-track Settings
 
Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage Tracks   (All Variation tracks)

Display mode:   

 All
Exome Avg Cover  Genome Aggregation Database (gnomAD) Average Exome Sample Coverage  Data version: Release 2.0.2
Exome Coverage %  Genome Aggregation Database (gnomAD) Percentage of Exome Samples with at least nX Coverage  Data version: Release 2.0.2
Genome Avg Cover  Genome Aggregation Database (gnomAD) Average Genome Sample Coverage  Data version: Release 2.0.2
Genome Coverage %  Genome Aggregation Database (gnomAD) Percentage of Genome Samples with at least nX Coverage  Data version: Release 2.0.2
Data version: Release 2.0.2

Description

The gnomAD tracks show variants from 123,136 exomes and 15,496 whole genomes of unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD), release 2.0.2. Raw data from all studies have been reprocessed through a unified pipeline and jointly variant-called to increase consistency across projects. For more information on the processing pipeline and population annotations, see the following blog post and the 2.0.2 README.

Display Conventions

For the Coverage subtracks:
  • The Average Sample Coverage graphs display the mean and median read depth of the samples at each position.
  • The nX Coverage Percentage graphs display the percentage of samples whose read depth is at least 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, and 100X.

  • For the Variants subtracks:
  • In mode, a vertical line is drawn at the position of each variant.
  • In mode, "ref" and "alt" alleles are displayed to the left of a vertical line with colored portions corresponding to allele counts. Hovering the mouse pointer over a variant pops up a display of alleles and counts.
  • The details for variants include extensive tag=value annotations extracted from the INFO column of gnomAD VCF files, listed under the label "INFO column annotations". The tags beginning with GC list genotype counts in an order that is fairly intuitive when a variant has two alleles: homozygous reference, heterozygous, homozygous alternate. However, when there are multiple alternate alleles, the number of combinations increases and the order of genotypes listed is a bit more complicated. If the alternate alleles are named alt1, alt2, alt3, ... altN, then the order of genotype counts follows this pattern:

    ref/ref,
    ref/alt1, alt1/alt1,
    ref/alt2, alt1/alt2, alt2/alt2,
    ref/alt3, alt1/alt3, alt2/alt3, alt3/alt3,
    ...
    ref/altN, alt1/altN, alt2/altN, alt3/altN, ..., altN/altN

    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.

    Credits

    Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (OBdL) 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 17;536(7616):285-91. PMID: 27535533; PMC: PMC5018207