Source data version: Release 3.0 (October 16, 2019)
Description
The gnomAD v3 track shows variants and derived information from 71,702 whole genomes (and no exomes), all mapped to the
GRCh38/hg38 reference sequence. Most of the genomes from v2 are included in v3. For more detailed
information on gnomAD v3, see the related blog post.
The gnomAD v2 tracks show variants from 125,748 exomes and 15,708 whole genomes, all mapped to
the GRCh37/hg19 reference sequence and lifted to the GRCh38/hg38 assembly. The data originate
from 141,456 unrelated individuals sequenced as part of various population-genetic and
disease-specific studies
collected by the Genome Aggregation Database (gnomAD), release 2.1.1.
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 2.1.1 README.
gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the
GRCh38/hg38 lift-over provided by gnomAD on their downloads site.
On hg38 only, a subtrack "Gnomad mutational constraint" captures the
depletion of variation caused by purifying natural selection.
This is similar to negative selection on loss-of-function (LoF) for genes, but
can be calculated for non-coding regions, too. Briefly, for any 1kbp window in
the genome, a model based on trinucleotide sequence context, base-level
methylation, and regional genomic features predicts expected number of mutations,
and compares this number to the observed number of mutations using a Z-score (see preprint
in the Reference section for details). The chrX scores were added as received from the authors,
as there are no mutations available for chrX, they are more speculative than the ones on the autosomes.
For questions on the gnomAD data, also see the gnomAD FAQ.
Display Conventions
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.
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
and constraint scores for the genome are in bigWig files in
the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory.
The mutational constraints score was updated in October 2022 from a previous,
now deprecated, pre-publication version. The old version can be found in our
archive
directory on the download server. It can be loaded by copying the URL into
our "Custom tracks" input box.
US Server