gnomAD gnomAD Coverage Track Settings
 
Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage

Track collection: Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint

+  Description
+  All tracks in this collection (5)

Maximum display mode:       Reset to defaults

Overlay method:
Type of graph:
Track height: pixels (range: 8 to 100)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 1)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
Select views (Help):
GenomesAverage ▾       ExomesAverage ▾       GenomesReadDepth ▾       ExomesReadDepth ▾      
List subtracks: only selected/visible    all    ()  
hide
 Configure
 Sample % > 1X  gnomAD Percentage of Genome Samples with at least 1X Coverage   Schema 
hide
 Configure
 Sample % > 1X  gnomAD Percentage of Exome Samples with at least 1X Coverage   Schema 
hide
 Configure
 Sample % > 5X  gnomAD Percentage of Genome Samples with at least 5X Coverage   Schema 
hide
 Configure
 Sample % > 5X  gnomAD Percentage of Exome Samples with at least 5X Coverage   Schema 
hide
 Configure
 Sample % > 10X  gnomAD Percentage of Genome Samples with at least 10X Coverage   Schema 
hide
 Configure
 Sample % > 10X  gnomAD Percentage of Exome Samples with at least 10X Coverage   Schema 
hide
 Configure
 Sample % > 15X  gnomAD Percentage of Genome Samples with at least 15X Coverage   Schema 
hide
 Configure
 Sample % > 15X  gnomAD Percentage of Exome Samples with at least 15X Coverage   Schema 
hide
 Configure
 Sample % > 20X  gnomAD Percentage of Genome Samples with at least 20X Coverage   Schema 
hide
 Configure
 Sample % > 20X  gnomAD Percentage of Exome Samples with at least 20X Coverage   Schema 
hide
 Configure
 Sample % > 25X  gnomAD Percentage of Genome Samples with at least 25X Coverage   Schema 
hide
 Configure
 Sample % > 25X  gnomAD Percentage of Exome Samples with at least 25X Coverage   Schema 
hide
 Configure
 Sample % > 30X  gnomAD Percentage of Genome Samples with at least 30X Coverage   Schema 
hide
 Configure
 Sample % > 30X  gnomAD Percentage of Exome Samples with at least 30X Coverage   Schema 
hide
 Configure
 Sample % > 50X  gnomAD Percentage of Genome Samples with at least 50X Coverage   Schema 
hide
 Configure
 Sample % > 50X  gnomAD Percentage of Exome Samples with at least 50X Coverage   Schema 
hide
 Configure
 Sample % > 100X  gnomAD Percentage of Genome Samples with at least 100X Coverage   Schema 
hide
 Configure
 Sample % > 100X  gnomAD Percentage of Exome Samples with at least 100X Coverage   Schema 
dense
 Configure
 Mean Coverage  gnomAD Mean Genome Sample Coverage   Schema 
dense
 Configure
 Mean Coverage  gnomAD Mean Exome Sample Coverage   Schema 
dense
 Configure
 Median Coverage  gnomAD Median Genome Sample Coverage   Schema 
dense
 Configure
 Median Coverage  gnomAD Median Exome Sample Coverage   Schema 
    
Data version: Release 2.0.2

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 (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 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