Resource

Id hg38/variant_frequencies/gnomAD_v2.1.1_liftover/genomescontent_copy
Type allele_score
Version 0
Summary Liftover of gnomAD genomes v2.1.1 to hg38.
Description
Labels
  • reference_genome: hg38/genomes/GRCh38-hg38

Scores (13)

ID Type Default annotation Description Histogram Range Summary
ID str

-
gnomAD v2.1.1 liftover genomes variant ID

No histogram: Too many unique values 101 for categorical histogram.

 NO DOMAIN
AC int

genome_gnomad_v2_1_1_ac
Alternative allele count in the whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR AC [0, 3.14e+04]
n
261,769,081
mean
378
sd
2.36e+03
AN int

genome_gnomad_v2_1_1_an
Total allele count in the whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR AN [0, 3.14e+04]
n
261,769,081
mean
2.97e+04
sd
4.71e+03
AF float

genome_gnomad_v2_1_1_af
Alternative allele frequency in the whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR AF [0, 1]
n
261,711,213
mean
0.0132
sd
0.079
AF_percent float

genome_gnomad_v2_1_1_af_percent
Alternative allele frequency in the whole gnomAD genome samples v2.1.1 as %
 HISTOGRAM FOR AF_percent [0, 100]
n
261,711,213
mean
1.32
sd
7.9
controls_AC int

genome_gnomad_v2_1_1_controls_ac
Alternative allele count in the controls subset of whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR controls_AC [0, 1.09e+04]
n
261,769,081
mean
129
sd
813
controls_AN int

genome_gnomad_v2_1_1_controls_an
gnomAD v2.1.1 liftover genome count of genotyped individuals in control group
 HISTOGRAM FOR controls_AN [0, 1.09e+04]
n
261,769,081
mean
1.02e+04
sd
1.75e+03
controls_AF float

-
Alternative allele frequency in the controls subset of whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR controls_AF [0, 1]
n
261,687,471
mean
0.0132
sd
0.0793
controls_AF_percent float

genome_gnomad_v2_1_1_controls_af_percent
Alternative allele frequency in the controls subset of whole gnomAD genome samples v2.1.1 as %
 HISTOGRAM FOR controls_AF_percent [0, 100]
n
261,687,471
mean
1.32
sd
7.93
non_neuro_AC int

genome_gnomad_v2_1_1_non_neuro_ac
Alternative allele count in the non-neuro subset of whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR non_neuro_AC [0, 2.13e+04]
n
261,769,081
mean
253
sd
1.61e+03
non_neuro_AN int

genome_gnomad_v2_1_1_non_neuro_an
Total allele count in the non-neuro subset of whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR non_neuro_AN [0, 2.13e+04]
n
261,769,081
mean
2.02e+04
sd
3.13e+03
non_neuro_AF float

-
Alternative allele frequency in the non-neuro subset of whole gnomAD genome samples v2.1.1
 HISTOGRAM FOR non_neuro_AF [0, 1]
n
261,704,006
mean
0.013
sd
0.0795
non_neuro_AF_percent float

genome_gnomad_v2_1_1_non_neuro_af_percent
Alternative allele frequency in the non-neuro subset of whole gnomAD genome samples v2.1.1 as %
 HISTOGRAM FOR non_neuro_AF_percent [0, 100]
n
261,704,006
mean
1.3
sd
7.95

n counts alleles; sd is the population standard deviation.

Alleles

Chromosome Alleles substitution % insertion % deletion % complex % other %
all chromosomes 261769081 87.28% 5.11% 7.61% <0.01% <0.01%
chr1 20211888 87.18% 5.20% 7.62% <0.01% 0.00%
chr1_KI270706v1_random 20523 92.22% 2.91% 4.86% <0.01% 0.00%
chr1_KI270711v1_random 22 95.45% 0.00% 4.55% 0.00% 0.00%
chr1_KI270712v1_random 30 86.67% 6.67% 6.67% 0.00% 0.00%
chr1_KI270765v1_alt 618 91.26% 4.85% 3.88% 0.00% 0.00%
chr1_KI270766v1_alt 2110 86.35% 5.17% 8.48% 0.00% 0.00%
chr2 21871319 87.46% 4.95% 7.58% <0.01% 0.00%
chr2_GL383522v1_alt 5 100.00% 0.00% 0.00% 0.00% 0.00%
chr2_KI270772v1_alt 416 73.56% 13.70% 12.74% 0.00% 0.00%
chr2_KI270773v1_alt 820 55.61% 16.34% 28.05% 0.00% 0.00%
chr2_KI270776v1_alt 96 72.92% 3.12% 23.96% 0.00% 0.00%
chr2_KI270894v1_alt 6727 85.91% 6.21% 7.88% 0.00% 0.00%
chr3 17827232 87.64% 4.93% 7.44% <0.01% 0.00%
chr4 17421774 87.56% 4.91% 7.53% <0.01% 0.00%
chr4_GL000008v2_random 25316 92.70% 2.38% 4.92% 0.00% 0.00%
chr5 16289994 87.64% 4.87% 7.49% <0.01% 0.00%
chr6 15185945 87.13% 5.15% 7.71% <0.01% 0.00%
chr6_KI270801v1_alt 8 87.50% 0.00% 12.50% 0.00% 0.00%
chr7 14714343 87.01% 5.20% 7.79% <0.01% 0.00%
chr7_KI270803v1_alt 25769 88.02% 5.72% 6.26% 0.00% 0.00%
chr8 14062590 88.30% 4.63% 7.07% <0.01% 0.00%
chr8_KI270811v1_alt 4 75.00% 25.00% 0.00% 0.00% 0.00%
chr8_KI270821v1_alt 5332 84.32% 5.18% 10.50% 0.00% 0.00%
chr9 11460554 87.87% 4.90% 7.23% <0.01% 0.00%
chr10 12113545 87.14% 5.19% 7.67% <0.01% 0.00%
chr11 12342012 87.76% 4.90% 7.34% <0.01% <0.01%
chr11_KI270927v1_alt 77 67.53% 7.79% 24.68% 0.00% 0.00%
chr12 11931143 86.75% 5.33% 7.91% <0.01% 0.00%
chr12_GL877875v1_alt 177 88.70% 4.52% 6.78% 0.00% 0.00%
chr13 8691936 87.06% 5.12% 7.81% <0.01% 0.00%
chr14 8202969 87.23% 5.13% 7.64% <0.01% 0.00%
chr14_GL000009v2_random 42164 93.15% 2.29% 4.56% 0.00% 0.00%
chr14_KI270726v1_random 24 83.33% 4.17% 12.50% 0.00% 0.00%
chr14_KI270846v1_alt 1384 88.37% 6.72% 4.91% 0.00% 0.00%
chr15 7714848 87.06% 5.24% 7.70% <0.01% 0.00%
chr15_KI270849v1_alt 14 92.86% 7.14% 0.00% 0.00% 0.00%
chr15_KI270850v1_alt 4956 83.78% 5.65% 10.57% 0.00% 0.00%
chr15_KI270851v1_alt 54 77.78% 9.26% 12.96% 0.00% 0.00%
chr15_KI270852v1_alt 81 85.19% 6.17% 8.64% 0.00% 0.00%
chr16 8618710 87.82% 4.97% 7.21% <0.01% 0.00%
chr17 7360952 85.90% 5.88% 8.22% <0.01% 0.00%
chr17_KI270857v1_alt 1272 53.54% 17.22% 29.25% 0.00% 0.00%
chr17_KI270860v1_alt 6 33.33% 50.00% 16.67% 0.00% 0.00%
chr17_KI270862v1_alt 98 69.39% 18.37% 12.24% 0.00% 0.00%
chr17_KI270909v1_alt 3832 84.94% 5.87% 9.19% 0.00% 0.00%
chr18 6893267 87.19% 5.11% 7.70% <0.01% 0.00%
chr19 5977880 85.21% 6.26% 8.53% <0.01% 0.00%
chr19_KI270938v1_alt 1936 67.82% 13.22% 18.96% 0.00% 0.00%
chr20 5515661 87.01% 5.32% 7.67% <0.01% 0.00%
chr21 3495953 86.83% 5.25% 7.92% <0.01% <0.01%
chr22 3556934 86.32% 5.65% 8.03% <0.01% 0.00%
chr22_KI270731v1_random 21 71.43% 23.81% 4.76% 0.00% 0.00%
chr22_KI270875v1_alt 5 40.00% 0.00% 60.00% 0.00% 0.00%
chr22_KI270879v1_alt 3587 85.59% 5.35% 9.06% 0.00% 0.00%
chr22_KI270928v1_alt 60 78.33% 13.33% 8.33% 0.00% 0.00%
chrUn_KI270742v1 30192 91.45% 2.91% 5.63% 0.00% 0.00%
chrX 10129893 86.84% 5.34% 7.82% <0.01% 0.00%
chrY 3 100.00% 0.00% 0.00% 0.00% 0.00%

Substitution matrix

ref → alt A C G T
A0
0.00%
8932180
3.91%
31279062
13.69%
8916233
3.90%
C11904161
5.21%
0
0.00%
10664231
4.67%
42563896
18.63%
G42498596
18.60%
10675216
4.67%
0
0.00%
12213318
5.35%
T8670142
3.80%
31268043
13.69%
8874765
3.88%
0
0.00%
ts/tv
1.83
147,609,597 transitions / 80,850,246 transversions

Indel lengths

alleles min max mean median
insertions 13377184 1 672 6.2 2
deletions 19931880 1 374 5.7 2
insertion length histogram deletion length histogram

Complex alleles

reference length alternative length alleles % of complex
≥64 1 163 100.00%

Files

Filename Size md5
combine_result.sh 474.0 B fa851daf7398367cb2d9f5a1a5b4a503
extract_info.sh 424.0 B cf68020206b293f498e582ad7fc47086
genomic_resource.yaml 5.08 KB c7827241f92a482c3885febc717fb87c
gnomad.genomes.r2.1.1.extract.tsv.gz 11.52 GB ca9bac763bd3b6ad7f7b6410ac2846c2
gnomad.genomes.r2.1.1.extract.tsv.gz.tbi 2.56 MB c50b22d0e97b437426e3990ab2bb2dad
hists/genome_gnomad_v2_1_1_af_percent 2.8 KB 1d048123f42ccf1a078863373184cdd0
hists/genome_gnomad_v2_1_1_af_percent.hist.toml 163.0 B c11fd0ed93eea3cf4d3c411d8ec991d4
statistics/