Resource

Id hg38/variant_frequencies/gnomAD_v2.1.1_liftover/exomescontent_copy
Type allele_score
Version 0
Summary Liftover of gnomAD exomes 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 exomes variant ID

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

 NO DOMAIN
AC int

exome_gnomad_v2_1_1_ac
Alternative allele count in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AC [0, 2.51e+05]
n
17,201,296
mean
457
sd
7.24e+03
AN int

exome_gnomad_v2_1_1_an
Total allele count in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AN [0, 2.51e+05]
n
17,201,296
mean
2.19e+05
sd
5.17e+04
AF float

exome_gnomad_v2_1_1_af
Alternative allele frequency in the whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR AF [0, 1]
n
17,197,102
mean
0.00237
sd
0.0344
AF_percent float

exome_gnomad_v2_1_1_af_percent
Alternative allele frequency in the whole gnomAD exome samples v2.1.1 as %
 HISTOGRAM FOR AF_percent [0, 100]
n
17,197,102
mean
0.237
sd
3.44
controls_AC int

exome_gnomad_v2_1_1_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
17,201,296
mean
198
sd
3.15e+03
controls_AN int

exome_gnomad_v2_1_1_controls_an
gnomAD v2.1.1 liftover exomes count of genotyped individuals in control group
 HISTOGRAM FOR controls_AN [0, 1.09e+05]
n
17,201,296
mean
9.53e+04
sd
2.32e+04
controls_AF float

-
Alternative allele frequency in the controls subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR controls_AF [0, 1]
n
17,189,940
mean
0.00236
sd
0.0344
controls_AF_percent float

exome_gnomad_v2_1_1_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
17,189,940
mean
0.236
sd
3.44
non_neuro_AC int

exome_gnomad_v2_1_1_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
17,201,296
mean
380
sd
5.99e+03
non_neuro_AN int

exome_gnomad_v2_1_1_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
17,201,296
mean
1.82e+05
sd
4.25e+04
non_neuro_AF float

-
Alternative allele frequency in the non-neuro subset of whole gnomAD exome samples v2.1.1
 HISTOGRAM FOR non_neuro_AF [0, 1]
n
17,194,887
mean
0.00237
sd
0.0344
non_neuro_AF_percent float

exome_gnomad_v2_1_1_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
17,194,887
mean
0.237
sd
3.44

n counts alleles; sd is the population standard deviation.

Alleles

Chromosome Alleles substitution % insertion % deletion % complex % other %
all chromosomes 17201296 93.14% 2.41% 4.45% <0.01% 0.00%
chr1 1705838 93.22% 2.32% 4.46% <0.01% 0.00%
chr1_KI270706v1_random 33 93.94% 0.00% 6.06% 0.00% 0.00%
chr1_KI270711v1_random 10 100.00% 0.00% 0.00% 0.00% 0.00%
chr1_KI270766v1_alt 63 92.06% 0.00% 7.94% 0.00% 0.00%
chr2 1230527 93.09% 2.40% 4.51% 0.00% 0.00%
chr3 958741 92.86% 2.54% 4.60% <0.01% 0.00%
chr4 642063 92.63% 2.58% 4.79% 0.00% 0.00%
chr4_GL000008v2_random 27 96.30% 3.70% 0.00% 0.00% 0.00%
chr5 740613 92.97% 2.44% 4.59% 0.00% 0.00%
chr6 835189 92.74% 2.60% 4.66% 0.00% 0.00%
chr7 839286 93.13% 2.42% 4.45% 0.00% 0.00%
chr7_KI270803v1_alt 5278 93.26% 2.77% 3.98% 0.00% 0.00%
chr8 620937 93.36% 2.36% 4.28% 0.00% 0.00%
chr9 713143 93.40% 2.31% 4.28% 0.00% 0.00%
chr10 665474 93.07% 2.42% 4.51% 0.00% 0.00%
chr11 1044308 93.38% 2.36% 4.26% <0.01% 0.00%
chr12 888857 92.82% 2.52% 4.66% 0.00% 0.00%
chr13 287634 92.40% 2.63% 4.97% 0.00% 0.00%
chr14 587175 92.97% 2.47% 4.56% 0.00% 0.00%
chr14_GL000009v2_random 25 100.00% 0.00% 0.00% 0.00% 0.00%
chr14_KI270846v1_alt 383 96.61% 2.61% 0.78% 0.00% 0.00%
chr15 610181 93.10% 2.45% 4.45% 0.00% 0.00%
chr15_KI270850v1_alt 730 77.95% 8.36% 13.70% 0.00% 0.00%
chr15_KI270851v1_alt 9 77.78% 0.00% 22.22% 0.00% 0.00%
chr16 865982 93.71% 2.23% 4.07% 0.00% 0.00%
chr17 1031179 93.17% 2.43% 4.39% 0.00% 0.00%
chr17_KI270857v1_alt 58 94.83% 3.45% 1.72% 0.00% 0.00%
chr17_KI270909v1_alt 364 93.13% 2.75% 4.12% 0.00% 0.00%
chr18 253274 92.89% 2.56% 4.56% 0.00% 0.00%
chr19 1229856 93.32% 2.33% 4.35% <0.01% 0.00%
chr19_KI270938v1_alt 943 95.65% 2.01% 2.33% 0.00% 0.00%
chr20 429532 93.40% 2.34% 4.27% 0.00% 0.00%
chr21 187586 92.80% 2.59% 4.61% 0.00% 0.00%
chr22 416083 93.61% 2.27% 4.12% 0.00% 0.00%
chr22_KI270879v1_alt 500 92.00% 2.60% 5.40% 0.00% 0.00%
chr22_KI270928v1_alt 20 70.00% 15.00% 15.00% 0.00% 0.00%
chrX 402541 93.45% 2.38% 4.18% 0.00% 0.00%
chrY 6854 92.88% 2.54% 4.58% 0.00% 0.00%

Substitution matrix

ref → alt A C G T
A0
0.00%
509653
3.18%
1771397
11.06%
430797
2.69%
C946005
5.90%
0
0.00%
945568
5.90%
3415745
21.32%
G3415874
21.32%
939885
5.87%
0
0.00%
938993
5.86%
T426728
2.66%
1771199
11.06%
509042
3.18%
0
0.00%
ts/tv
1.84
10,374,215 transitions / 5,646,671 transversions

Indel lengths

alleles min max mean median
insertions 415095 1 621 5.81 2
deletions 765309 1 297 4.62 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
combine_result.sh 473.0 B ea6255336bf53460c5c56ce1e9d8fa92
extract_info.sh 467.0 B 73f562dcc4f646d5566f2e4adc4d5990
genomic_resource.yaml 5.07 KB df18a9e6167f9f9b9c8272cfe21e4cb7
gnomad.exomes.r2.1.1.extract.tsv.gz 927.36 MB f83f0702a0de977407f1220e6d40a19b
gnomad.exomes.r2.1.1.extract.tsv.gz.tbi 733.7 KB 6713e81d71d66f5eec813e9c709100ac
hists/exome_gnomad_v2_1_1_af_percent 2.68 KB 6955afb1beee3fa319256ba6640397bd
hists/exome_gnomad_v2_1_1_af_percent.hist.toml 163.0 B c11fd0ed93eea3cf4d3c411d8ec991d4
statistics/