Resource
| Id | hg38/cnv_collections/gnomAD.v4.1_Genome_SV |
|---|---|
| Type | fragment_score |
| Version | 0 |
| Summary | gnomAD v4.1 Genome SV collection |
| Description |
The gnomAD v4 Genome Structural Variant (SV) Collection is a comprehensive resource cataloging structural variations across human genomes, derived from whole-genome sequencing data. This dataset represents one of the largest publicly available SV collections, encompassing deletions, duplications, insertions, inversions, and translocations (including complex rearrangements labeled as BND). By integrating data from diverse populations, gnomAD v4 aims to provide a detailed view of SV diversity, frequency, and distribution in the human genome, enabling researchers to better understand the role of structural variations in health and disease. For more information: https://gnomad.broadinstitute.org/news/2023-11-v4-structural-variants/ Collins et al, A structural variation reference for medical and population genetics, Nature 2020 Downloaded on 01/07/2025 from https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/genome_sv/gnomad.v4.1.sv.sites.vcf.gz DataPrep.py converts vcf file to GRR format (only taking deletion and duplications, dropping records where two ends of an SV are on different chromosomes) and creates genomic_resource.yaml file. |
| Labels |
Scores (30)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| deletion_duplication | str |
deletion_duplication |
duplication or deletion
|
 |
deletion, duplication | |
| cnv_name | str |
cnv_name |
Handy name to refer to the CNV.
|
No histogram: Too many unique values 101 for categorical histogram. |
NO DOMAIN | |
| SVLEN | int |
SVLEN |
SV length
|
 |
[50, 2.22e+08] |
|
| AN | int |
AN |
Total number of alleles genotyped (biallelic sites only).
|
 |
[1, 1.26e+05] |
|
| AC | int |
AC |
Number of non-reference alleles observed (biallelic sites only).
|
 |
[1, 1.26e+05] |
|
| AF | float |
AF |
Allele frequency (biallelic sites only).
|
 |
[8e-06, 1] |
|
| AN_afr | int |
AN_afr |
Total number of African-American alleles genotyped (biallelic sites only).
|
 |
[0, 3.38e+04] |
|
| AN_amr | int |
AN_amr |
Total number of Latino alleles genotyped (biallelic sites only).
|
 |
[0, 1.26e+04] |
|
| AN_asj | int |
AN_asj |
Total number of Ashkenazi Jewish alleles genotyped (biallelic sites only).
|
 |
[0, 3.18e+03] |
|
| AN_eas | int |
AN_eas |
Total number of East Asian alleles genotyped (biallelic sites only).
|
 |
[0, 4.05e+03] |
|
| AN_fin | int |
AN_fin |
Total number of Finnish alleles genotyped (biallelic sites only).
|
 |
[0, 6.48e+03] |
|
| AN_mid | int |
AN_mid |
Total number of Middle Eastern alleles genotyped (biallelic sites only).
|
 |
[0, 64] |
|
| AN_nfe | int |
AN_nfe |
Total number of Non-Finnish European alleles genotyped (biallelic sites only).
|
 |
[0, 5.91e+04] |
|
| AN_sas | int |
AN_sas |
Total number of South Asian alleles genotyped (biallelic sites only).
|
 |
[0, 4.41e+03] |
|
| AC_afr | int |
AC_afr |
Number of non-reference African-American alleles observed (biallelic sites only).
|
 |
[0, 3.38e+04] |
|
| AC_amr | int |
AC_amr |
Number of non-reference Latino alleles observed (biallelic sites only).
|
 |
[0, 1.26e+04] |
|
| AC_asj | int |
AC_asj |
Number of non-reference Ashkenazi Jewish alleles observed (biallelic sites only).
|
 |
[0, 3.18e+03] |
|
| AC_eas | int |
AC_eas |
Number of non-reference East Asian alleles observed (biallelic sites only).
|
 |
[0, 4.05e+03] |
|
| AC_fin | int |
AC_fin |
Number of non-reference Finnish alleles observed (biallelic sites only).
|
 |
[0, 6.48e+03] |
|
| AC_mid | int |
AC_mid |
Number of non-reference Middle Eastern alleles observed (biallelic sites only).
|
 |
[0, 64] |
|
| AC_nfe | int |
AC_nfe |
Number of non-reference Non-Finnish European alleles observed (biallelic sites only).
|
 |
[0, 5.91e+04] |
|
| AC_sas | int |
AC_sas |
Number of non-reference South Asian alleles observed (biallelic sites only).
|
 |
[0, 4.41e+03] |
|
| AF_afr | float |
AF_afr |
African-American allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_amr | float |
AF_amr |
Latino allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_asj | float |
AF_asj |
Ashkenazi Jewish allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_eas | float |
AF_eas |
East Asian allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_fin | float |
AF_fin |
Finnish allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_mid | float |
AF_mid |
Middle Eastern allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_nfe | float |
AF_nfe |
Non-Finnish European allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
| AF_sas | float |
AF_sas |
South Asian allele frequency (biallelic sites only).
|
 |
[0, 1] |
|
n counts fragments; sd is the population standard deviation.
Fragments
| Chromosome | Fragments |
|---|---|
| all chromosomes | 1475604 |
| chr1 | 114126 |
| chr2 | 113083 |
| chr3 | 88906 |
| chr4 | 85186 |
| chr5 | 82424 |
| chr6 | 81328 |
| chr7 | 89619 |
| chr8 | 68822 |
| chr9 | 61560 |
| chr10 | 68389 |
| chr11 | 68325 |
| chr12 | 68599 |
| chr13 | 44649 |
| chr14 | 45098 |
| chr15 | 40489 |
| chr16 | 54624 |
| chr17 | 55098 |
| chr18 | 35812 |
| chr19 | 55127 |
| chr20 | 35325 |
| chr21 | 24735 |
| chr22 | 27146 |
| chrX | 60050 |
| chrY | 7084 |
Fragment lengths
| fragments | min | max | mean | median | |
|---|---|---|---|---|---|
| fragments | 1475604 | 51 | 222470488 | 25103.16 | 607 |
Files
| Filename | Size | md5 |
|---|---|---|
| DataPrep.py | 7.58 KB | ba2d4e268414810cba7614ed25289307 |
| genomic_resource.yaml | 5.27 KB | 25f1f8dca4f39f7ed9107c6c082d8051 |
| gnomad.v4.1.sv.sites.tsv.gz | 81.92 MB | a16e3fde2366c6e849990a4083f26993 |
| gnomad.v4.1.sv.sites.tsv.gz.tbi | 48.78 KB | 4bd2c5f592a2a11a7437acd66733c370 |
| gnomad.v4.1.sv.sites.vcf | 11.88 GB | 59ee22c4615e584d3d663a2af37b9e84 |
| statistics/ |