Description
The Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage track
set shows various read-depth variant metrics calculated separately for exomes and genomes on a ~10%
subset of the v2.0.2 samples. Multiple exome capture methods and sequencing chemistries were used
for sequencing, so coverage varies between individuals across sites. This variation of coverage is
incorporated in this track.
This track includes several subtracks of average coverage metrics and sample percentage of coverage.
For more information on the processing pipeline and population annotations, see the following
blog post
and the 2.0.2 README.
Display Conventions
The Average Sample Coverage graphs 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 graphs 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.
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
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