Database: hg38 Primary Table: gnomadGenomesVariantsV3 VCF File: /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz Format description: The fields of a Variant Call Format data line See the Variant Call Format specification for more details
An identifier from the reference genome
The reference position, with the 1st base having position 1
Semi-colon separated list of unique identifiers where available
Comma separated list of alternate non-reference alleles called on at least one of the samples
Phred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong)
PASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail
Additional information encoded as a semicolon-separated series of short keys with optional comma-separated values
If genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT
If genotype columns are specified in header, a tab-separated set of genotype column values; each value is a colon-separated list of values corresponding to keys in the format column
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
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 disruptive 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.
In mode, a vertical line is drawn at the position of
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 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.