Resource
| Id | hg19/variant_frequencies/gnomAD_v2.1.1/genomes |
|---|---|
| Type | allele_score |
| Version | 0 |
| Summary | gnomAD genomes v2.1.1 variants build from ~32,000 whole genome sequencing samples published by the Broad Institute. |
| Description |
gnomAD genomes v2.1.1 liftoverOriginal gnomAD genomes v2.1.1 liftover is downloaded on October 19, 2020 from https://gnomad.broadinstitute.org/. tabix -s 1 -b 2 -e 2 -f gnomad..r2.1.1.extract.tsv.gz |
| Labels |
|
Scores (13)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ID | str |
- |
variant ID
|
No histogram: Too many unique values 101 for categorical histogram. |
NO DOMAIN | |
| AC | int |
genome_gnomad_ac |
Alternative allele count in the whole gnomAD genome samples v2.1.1
|
 |
[0, 3.14e+04] |
|
| AN | int |
genome_gnomad_an |
Total allele count in the whole gnomAD genome samples v2.1.1
|
 |
[0, 3.14e+04] |
|
| AF | float |
genome_gnomad_af |
Alternative allele frequency in the whole gnomAD genome samples v2.1.1
|
 |
[0, 1] |
|
| AF_percent | float |
genome_gnomad_af_percent |
Alternative allele frequency in the whole gnomAD genome samples v2.1.1 as %
|
 |
[0, 100] |
|
| controls_AC | int |
genome_gnomad_controls_ac |
Alternative allele count in the controls subset of whole gnomAD genome samples v2.1.1
|
 |
[0, 1.09e+04] |
|
| controls_AN | int |
genome_gnomad_controls_an |
gnomAD v2.1.1 liftover genome count of genotyped individuals in control group
|
 |
[0, 1.09e+04] |
|
| controls_AF | float |
genome_gnomad_controls_af |
Alternative allele frequency in the controls subset of whole gnomAD genome samples v2.1.1
|
 |
[0, 1] |
|
| controls_AF_percent | float |
genome_gnomad_controls_af_percent |
Alternative allele frequency in the controls subset of whole gnomAD genome samples v2.1.1 as %
|
 |
[0, 100] |
|
| non_neuro_AC | int |
genome_gnomad_non_neuro_ac |
Alternative allele count in the non-neuro subset of whole gnomAD genome samples v2.1.1
|
 |
[0, 2.13e+04] |
|
| non_neuro_AN | int |
genome_gnomad_non_neuro_an |
Total allele count in the non-neuro subset of whole gnomAD genome samples v2.1.1
|
 |
[0, 2.13e+04] |
|
| non_neuro_AF | float |
genome_gnomad_non_neuro_af |
Alternative allele frequency in the non-neuro subset of whole gnomAD genome samples v2.1.1
|
 |
[0, 1] |
|
| non_neuro_AF_percent | float |
genome_gnomad_non_neuro_af_percent |
Alternative allele frequency in the non-neuro subset of whole gnomAD genome samples v2.1.1 as %
|
 |
[0, 100] |
|
n counts alleles; sd is the population standard deviation.
Alleles
| Chromosome | Alleles | substitution % | insertion % | deletion % | complex % | other % |
|---|---|---|---|---|---|---|
| all chromosomes | 261942305 | 87.26% | 5.11% | 7.63% | <0.01% | 0.00% |
| chr1 | 20370889 | 87.18% | 5.19% | 7.63% | <0.01% | 0.00% |
| chr2 | 21892244 | 87.45% | 4.95% | 7.60% | <0.01% | 0.00% |
| chr3 | 17834353 | 87.63% | 4.93% | 7.44% | <0.01% | 0.00% |
| chr4 | 17423638 | 87.55% | 4.91% | 7.53% | <0.01% | 0.00% |
| chr5 | 16290653 | 87.64% | 4.87% | 7.49% | <0.01% | 0.00% |
| chr6 | 15190439 | 87.13% | 5.15% | 7.72% | <0.01% | 0.00% |
| chr7 | 14752316 | 86.99% | 5.20% | 7.81% | <0.01% | 0.00% |
| chr8 | 14073573 | 88.29% | 4.64% | 7.08% | <0.01% | 0.00% |
| chr9 | 11480612 | 87.85% | 4.90% | 7.25% | <0.01% | 0.00% |
| chr10 | 12118749 | 87.13% | 5.19% | 7.68% | <0.01% | 0.00% |
| chr11 | 12345492 | 87.75% | 4.90% | 7.34% | <0.01% | 0.00% |
| chr12 | 11933433 | 86.75% | 5.33% | 7.91% | <0.01% | 0.00% |
| chr13 | 8693572 | 87.06% | 5.12% | 7.82% | <0.01% | 0.00% |
| chr14 | 8220636 | 87.20% | 5.13% | 7.67% | <0.01% | 0.00% |
| chr15 | 7723667 | 87.04% | 5.24% | 7.72% | <0.01% | 0.00% |
| chr16 | 8618655 | 87.82% | 4.97% | 7.21% | <0.01% | 0.00% |
| chr17 | 7373817 | 85.86% | 5.88% | 8.26% | <0.01% | 0.00% |
| chr18 | 6893749 | 87.19% | 5.11% | 7.70% | <0.01% | 0.00% |
| chr19 | 5991870 | 85.15% | 6.27% | 8.58% | <0.01% | 0.00% |
| chr20 | 5516836 | 87.00% | 5.32% | 7.68% | <0.01% | 0.00% |
| chr21 | 3483000 | 86.80% | 5.26% | 7.94% | <0.01% | 0.00% |
| chr22 | 3567085 | 86.27% | 5.66% | 8.08% | <0.01% | 0.00% |
| chrX | 10153027 | 86.77% | 5.35% | 7.88% | <0.01% | 0.00% |
Substitution matrix
| ref → alt | A | C | G | T |
|---|---|---|---|---|
| A | 0 0.00% | 8938211 3.91% | 31292254 13.69% | 8921837 3.90% |
| C | 11909624 5.21% | 0 0.00% | 10668705 4.67% | 42581756 18.63% |
| G | 42514377 18.60% | 10682011 4.67% | 0 0.00% | 12219768 5.35% |
| T | 8675331 3.80% | 31286762 13.69% | 8879545 3.88% | 0 0.00% |
ts/tv
1.83
147,675,149 transitions
/ 80,895,032 transversions
Indel lengths
| alleles | min | max | mean | median | |
|---|---|---|---|---|---|
| insertions | 13390268 | 1 | 672 | 6.2 | 2 |
| deletions | 19981681 | 1 | 374 | 5.73 | 2 |
×
×
Complex alleles
| reference length | alternative length | alleles | % of complex |
|---|---|---|---|
| ≥64 | 1 | 175 | 100.00% |
Files
| Filename | Size | md5 |
|---|---|---|
| genomic_resource.yaml | 5.14 KB | 5107cf9b045436a563e41278a533d12a |
| gnomad.genomes.r2.1.1.sites-exported.txt.gz | 12.27 GB | 3a6418c74dcce16a59ba1d9710935c7b |
| gnomad.genomes.r2.1.1.sites-exported.txt.gz.tbi | 2.57 MB | d3b2dc434e68537e5e7f19cae68477aa |
| statistics/ |