Resource
| Id | hg38/cnv_collections/gnomAD.v4.1_Exome_CNV |
|---|---|
| Type | fragment_score |
| Version | 0 |
| Summary | gnomAD v4.1 Exome CNV collection |
| Description |
The gnomAD v4 dataset includes rare (<1% overall site frequency) autosomal coding copy number variants (CNVs) discovered from exome sequencing (ES) of 464,297 individuals. Using the GATK-gCNV method, the dataset provides high-quality CNV calls, comprising 66,903 rare coding CNV sites, including deletions and duplications. These variants were annotated for their genic impact and frequency, offering insights into genetic diversity across various ancestry groups. For more information: https://gnomad.broadinstitute.org/news/2023-11-v4-copy-number-variants/ Downloaded on 01/07/2025 from https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/exome_cnv/gnomad.v4.1.cnv.all.vcf.gz DataPrep.py converts vcf file to GRR format 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
|
 |
duplication, deletion | |
| 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 |
Length of CNV
|
 |
[276, 1.03e+08] |
|
| SC | int |
SC |
Number of releasable samples with a variant at this site
|
 |
[1, 4.07e+03] |
|
| SN | int |
SN |
Total number of releasable samples considered at this site
|
 |
[1.32e+04, 4.64e+05] |
|
| SF | float |
SF |
Proportion of releasable samples (site frequency) with a variant at this site
|
 |
[2.15e-06, 0.00876] |
|
| SC_afr | int |
SC_afr |
Number of releasable AFR samples with a variant at this site
|
 |
[0, 1.28e+03] |
|
| SC_amr | int |
SC_amr |
Number of releasable AMR samples with a variant at this site
|
 |
[0, 258] |
|
| SC_asj | int |
SC_asj |
Number of releasable ASJ samples with a variant at this site
|
 |
[0, 551] |
|
| SC_eas | int |
SC_eas |
Number of releasable EAS samples with a variant at this site
|
 |
[0, 615] |
|
| SC_fin | int |
SC_fin |
Number of releasable FIN samples with a variant at this site
|
 |
[0, 725] |
|
| SC_mid | int |
SC_mid |
Number of releasable MID samples with a variant at this site
|
 |
[0, 79] |
|
| SC_nfe | int |
SC_nfe |
Number of releasable NFE samples with a variant at this site
|
 |
[0, 3.49e+03] |
|
| SC_sas | int |
SC_sas |
Number of releasable SAS samples with a variant at this site
|
 |
[0, 2.02e+03] |
|
| SN_afr | int |
SN_afr |
Total number of releasable AFR samples considered at this site
|
 |
[157, 1.13e+04] |
|
| SN_amr | int |
SN_amr |
Total number of releasable AMR samples considered at this site
|
 |
[253, 2.08e+04] |
|
| SN_asj | int |
SN_asj |
Total number of releasable ASJ samples considered at this site
|
 |
[128, 1.04e+04] |
|
| SN_eas | int |
SN_eas |
Total number of releasable EAS samples considered at this site
|
 |
[159, 1.59e+04] |
|
| SN_fin | int |
SN_fin |
Total number of releasable FIN samples considered at this site
|
 |
[106, 2.27e+04] |
|
| SN_mid | int |
SN_mid |
Total number of releasable MID samples considered at this site
|
 |
[23, 1.41e+03] |
|
| SN_nfe | int |
SN_nfe |
Total number of releasable NFE samples considered at this site
|
 |
[4.44e+03, 3.26e+05] |
|
| SN_sas | int |
SN_sas |
Total number of releasable SAS samples considered at this site
|
 |
[191, 3.45e+04] |
|
| SF_afr | float |
SF_afr |
Proportion of releasable AFR samples with a variant at this site
|
 |
[0, 0] |
|
| SF_amr | float |
SF_amr |
Proportion of releasable AMR samples with a variant at this site
|
 |
[0, 0] |
|
| SF_asj | float |
SF_asj |
Proportion of releasable ASJ samples with a variant at this site
|
 |
[0, 0] |
|
| SF_eas | float |
SF_eas |
Proportion of releasable EAS samples with a variant at this site
|
 |
[0, 0] |
|
| SF_fin | float |
SF_fin |
Proportion of releasable FIN samples with a variant at this site
|
 |
[0, 0] |
|
| SF_mid | float |
SF_mid |
Proportion of releasable MID samples with a variant at this site
|
 |
[0, 0] |
|
| SF_nfe | float |
SF_nfe |
Proportion of releasable NFE samples with a variant at this site
|
 |
[0, 0] |
|
| SF_sas | float |
SF_sas |
Proportion of releasable SAS samples with a variant at this site
|
 |
[0, 0] |
|
n counts fragments; sd is the population standard deviation.
Fragments
| Chromosome | Fragments |
|---|---|
| all chromosomes | 68699 |
| 1 | 6580 |
| 2 | 5117 |
| 3 | 4026 |
| 4 | 3268 |
| 5 | 3180 |
| 6 | 3431 |
| 7 | 3573 |
| 8 | 2770 |
| 9 | 2915 |
| 10 | 2780 |
| 11 | 3585 |
| 12 | 3705 |
| 13 | 1298 |
| 14 | 2057 |
| 15 | 2525 |
| 16 | 3401 |
| 17 | 3926 |
| 18 | 1260 |
| 19 | 5113 |
| 20 | 1685 |
| 21 | 802 |
| 22 | 1702 |
Fragment lengths
| fragments | min | max | mean | median | |
|---|---|---|---|---|---|
| fragments | 68699 | 277 | 103231396 | 148130.66 | ≥8192 |
Files
| Filename | Size | md5 |
|---|---|---|
| DataPrep.py | 8.02 KB | 415423728d5e7b5b370a5b78aab16474 |
| genomic_resource.yaml | 4.75 KB | cc1f152d021cd9cb0282f7496af5d965 |
| gnomad.v4.1.cnv.all.tsv.gz | 1.41 MB | 28f7745fa2269b5cbfccb2988d58d1e1 |
| gnomad.v4.1.cnv.all.tsv.gz.tbi | 28.86 KB | ef133dfef67c21169b7b362cd20b356b |
| gnomad.v4.1.cnv.all.vcf | 93.34 MB | 590aabdc6e5ee6f26893e87bc31817a1 |
| statistics/ |