Resource

Id hg19/variant_frequencies/gnomAD_v2.1.1/exomescontent_copy
Type allele_score
Version 0
Summary gnomAD exomes v2.1.1 variants build from ~260,000 whole exome samples published by the Broad Institute.
Description
Labels
  • reference_genome: hg19/genomes/ucsc-hg19

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

exome_gnomad_ac
Alternative allele count in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AC [0, 2.51e+05]
n
17,209,972
mean
469
sd
7.4e+03
AN int

exome_gnomad_an
Total allele count in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AN [0, 2.51e+05]
n
17,209,972
mean
2.19e+05
sd
5.17e+04
AF float

exome_gnomad_af
Alternative allele frequency in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AF [0, 1]
n
17,205,639
mean
0.00244
sd
0.0352
AF_percent float

exome_gnomad_af_percent
Alternative allele frequency in the whole gnomAD exome samples v2.1.1 as percent
 HISTOGRAM FOR AF_percent [0, 100]
n
17,205,639
mean
0.244
sd
3.52
controls_AC int

exome_gnomad_controls_ac
Alternative allele count in the controls subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR controls_AC [0, 1.09e+05]
n
17,209,972
mean
204
sd
3.22e+03
controls_AN int

exome_gnomad_controls_an
gnomAD v2.1.1 liftover exomes count of genotyped individuals in control group
 HISTOGRAM FOR controls_AN [0, 1.09e+05]
n
17,209,972
mean
9.53e+04
sd
2.32e+04
controls_AF float

exome_gnomad_controls_af
Alternative allele frequency in the controls subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR controls_AF [0, 1]
n
17,198,427
mean
0.00243
sd
0.0351
controls_AF_percent float

exome_gnomad_controls_af_percent
Alternative allele frequency in the controls subset of whole gnomAD exome samples v2.1.1 as %
 HISTOGRAM FOR controls_AF_percent [0, 100]
n
17,198,427
mean
0.243
sd
3.51
non_neuro_AC int

exome_gnomad_non_neuro_ac
Alternative allele count in the non-neuro subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR non_neuro_AC [0, 2.08e+05]
n
17,209,972
mean
390
sd
6.12e+03
non_neuro_AN int

exome_gnomad_non_neuro_an
Total allele count in the non-neuro subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR non_neuro_AN [0, 2.08e+05]
n
17,209,972
mean
1.82e+05
sd
4.25e+04
non_neuro_AF float

exome_gnomad_non_neuro_af
Alternative allele frequency in the non-neuro subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR non_neuro_AF [0, 1]
n
17,203,406
mean
0.00244
sd
0.0351
non_neuro_AF_percent float

exome_gnomad_non_neuro_af_percent
Alternative allele frequency in the non-neuro subset of whole gnomAD exome samples v2.1.1 as %
 HISTOGRAM FOR non_neuro_AF_percent [0, 100]
n
17,203,406
mean
0.244
sd
3.51

n counts alleles; sd is the population standard deviation.

Alleles

Chromosome Alleles substitution % insertion % deletion % complex % other %
all chromosomes 17209972 93.13% 2.41% 4.45% <0.01% 0.00%
chr1 1707147 93.21% 2.32% 4.47% <0.01% 0.00%
chr2 1230614 93.09% 2.40% 4.51% 0.00% 0.00%
chr3 958850 92.86% 2.54% 4.60% <0.01% 0.00%
chr4 642129 92.63% 2.58% 4.79% 0.00% 0.00%
chr5 740678 92.97% 2.44% 4.59% 0.00% 0.00%
chr6 835212 92.74% 2.60% 4.66% 0.00% 0.00%
chr7 845891 93.12% 2.42% 4.46% 0.00% 0.00%
chr8 621220 93.35% 2.36% 4.29% 0.00% 0.00%
chr9 713431 93.40% 2.31% 4.29% 0.00% 0.00%
chr10 665745 93.07% 2.42% 4.51% 0.00% 0.00%
chr11 1044543 93.38% 2.36% 4.26% <0.01% 0.00%
chr12 889014 92.82% 2.52% 4.67% 0.00% 0.00%
chr13 287655 92.40% 2.63% 4.97% 0.00% 0.00%
chr14 589647 92.96% 2.47% 4.57% 0.00% 0.00%
chr15 611216 93.04% 2.46% 4.50% 0.00% 0.00%
chr16 866022 93.71% 2.23% 4.07% 0.00% 0.00%
chr17 1031902 93.17% 2.43% 4.40% 0.00% 0.00%
chr18 253290 92.88% 2.56% 4.56% 0.00% 0.00%
chr19 1231680 93.31% 2.33% 4.36% <0.01% 0.00%
chr20 429586 93.40% 2.34% 4.27% 0.00% 0.00%
chr21 187702 92.78% 2.59% 4.63% 0.00% 0.00%
chr22 416866 93.59% 2.28% 4.13% 0.00% 0.00%
chrX 403070 93.43% 2.38% 4.19% 0.00% 0.00%
chrY 6862 92.82% 2.54% 4.65% 0.00% 0.00%

Substitution matrix

ref → alt A C G T
A0
0.00%
510035
3.18%
1771868
11.05%
431340
2.69%
C946359
5.90%
0
0.00%
946037
5.90%
3417149
21.32%
G3416493
21.32%
940406
5.87%
0
0.00%
939489
5.86%
T426834
2.66%
1772432
11.06%
509388
3.18%
0
0.00%
ts/tv
1.84
10,377,942 transitions / 5,649,888 transversions

Indel lengths

alleles min max mean median
insertions 415528 1 621 5.82 2
deletions 766608 1 297 4.65 2
insertion length histogram deletion length histogram

Complex alleles

reference length alternative length alleles % of complex
≥64 1 6 100.00%

Files

Filename Size md5
README.txt 1.59 KB 141f34e4f4dc70971dab151e710aec13
genomic_resource.yaml 5.03 KB a8580dd4638c29f9533c750a16e45050
gnomad.exomes.r2.1.1.sites-exported.txt.gz 958.54 MB cb1421eb09c7d88dc517d7421d7b3242
gnomad.exomes.r2.1.1.sites-exported.txt.gz.tbi 737.31 KB 2dd456d16db7056e6a87c282faa4cd14
statistics/