Version: Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020) Assembly: Human Dec. 2013 (GRCh38/hg38) Data last updated at UCSC: 2024-03-19 22:24:38
Description
gnomAD v3.1.1
gnomAD 3 was a genomes-only release. The gnomAD v3.1.1 track is the current version of gnomAD 3
and shows variants from 76,156 whole genomes (and no exomes), all mapped to the GRCh38/hg38
reference sequence. 4,454 genomes were added to the number of genomes in the previous v3 release.
For more detailed information on gnomAD v3.1, see the related blog post.
A bugfix to v3.1 resulted in gnomAD v3.1.1, see
changelog.
Do not use gnomAD v3.1 anymore, we will remove the 3.1 track soon.
gnomAD v3.1 (Deprecated)
The gnomAD v3.1 track is deprecated. Please use v3.1.1 instead.
gnomAD v3
The gnomAD v3 track shows variants from 71,702 whole genomes (and no exomes), all mapped to the
GRCh38/hg38 reference sequence. For more detailed
information on gnomAD v3, see the related blog post.
For questions on the gnomAD data, also see the gnomAD FAQ.
The gnomAD v3.1.1 track version follows the same conventions and configuration as the v3.1 track,
except as noted below.
There is a Non-cancer filter used to exclude/include variants from samples of individuals who
were not ascertained for having cancer in a cancer study.
There are additional FILTER field filters: AS_VQSR, indel_stack (chrM only), and npg (chrM only).
Where possible, variants overlapping multiple transcripts/genes have been collapsed into one
variant, with additional information available on the details page, which has roughly halved the
number of items in the bigBed.
The bigBed has been split into two files, one with the information necessary for the track
display, and one with the information necessary for the details page. For more information on
this data format, please see the Data Access section below.
The VEP annotation is shown as a table instead of spread across multiple fields.
Intergenic variants have not been pre-filtered.
gnomAD v3.1
By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters
described below), before the track switches to dense display mode.
Mouse hover on an item will display many details about each variant, including the affected gene(s),
the variant type, and annotation (missense, synonymous, etc).
Clicking on an item will display additional details on the variant, including a population frequency
table showing allele count in each sub-population.
Following the conventions on the gnomAD browser, items are shaded according to their Annotation
type:
pLoF
Missense
Synonymous
Other
Label Options
To maintain consistency with the gnomAD website, variants are by default labeled according
to their chromosomal start position followed by the reference and alternate alleles,
for example "chr1-1234-T-CAG". dbSNP rsID's are also available as an additional
label, if the variant is present in dbSnp.
Filtering Options
Three filters are available for these tracks:
FILTER: Used to exclude/include variants that failed Random Forest
(RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The
PASS option is used to include/exclude variants that pass all of the RF,
InbreedingCoeff, and AC0 filters, as denoted in the original VCF.
Annotation type: Used to exclude/include variants that are annotated as
Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as
annotated by VEP version 85 (GENCODE v19).
Variant Type: Used to exclude/include variants according to the type of
variation, as annotated by VEP v85.
There is one additional configurable filter on the minimum minor allele frequency.
For the v3.1.1 variants in particular, the underlying bigBed only contains enough information
necessary to use the track in the browser. The extra data like VEP annotations and CADD scores are
available in the same directory
as the bigBed but in the files gnomad.v3.1.1.details.tab.gz and
gnomad.v3.1.1.details.tab.gz.gzi. The gnomad.v3.1.1.details.tab.gz contains the gzip
compressed extra data in JSON format, and the .gzi file is available to speed searching of
this data. Each variant has an associated md5sum in the name field of the bigBed which can be
used along with the _dataOffset and _dataLen fields to get the associated external data, as show
below:
# find item of interest:
bigBedToBed genomes.bb stdout | head -4 | tail -1
chr1 12416 12417 854246d79dc5d02dcdbd5f5438542b6e [..omitted for brevity..] chr1-12417-G-A 67293 902
# use the final two fields, _dataOffset and _dataLen (add one to _dataLen to include a newline), to get the extra data:
bgzip -b 67293 -s 903 gnomad.v3.1.1.details.tab.gz
854246d79dc5d02dcdbd5f5438542b6e {"DDX11L1": {"cons": ["non_coding_transcript_variant", [..omitted for brevity..]