gnomad_annotation_pext
Versions: 2.1.1
Reference genome builds: GRCh37
Type:
hail.Table
Schema (2.1.1, GRCh37)
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Global fields:
None
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Row fields:
'context': str
'vep': struct {
assembly_name: str,
allele_string: str,
ancestral: str,
colocated_variants: array<struct {
aa_allele: str,
aa_maf: float64,
afr_allele: str,
afr_maf: float64,
allele_string: str,
amr_allele: str,
amr_maf: float64,
clin_sig: array<str>,
end: int32,
eas_allele: str,
eas_maf: float64,
ea_allele: str,
ea_maf: float64,
eur_allele: str,
eur_maf: float64,
exac_adj_allele: str,
exac_adj_maf: float64,
exac_allele: str,
exac_afr_allele: str,
exac_afr_maf: float64,
exac_amr_allele: str,
exac_amr_maf: float64,
exac_eas_allele: str,
exac_eas_maf: float64,
exac_fin_allele: str,
exac_fin_maf: float64,
exac_maf: float64,
exac_nfe_allele: str,
exac_nfe_maf: float64,
exac_oth_allele: str,
exac_oth_maf: float64,
exac_sas_allele: str,
exac_sas_maf: float64,
id: str,
minor_allele: str,
minor_allele_freq: float64,
phenotype_or_disease: int32,
pubmed: array<int32>,
sas_allele: str,
sas_maf: float64,
somatic: int32,
start: int32,
strand: int32
}>,
context: str,
end: int32,
id: str,
input: str,
intergenic_consequences: array<struct {
allele_num: int32,
consequence_terms: array<str>,
impact: str,
minimised: int32,
variant_allele: str
}>,
most_severe_consequence: str,
motif_feature_consequences: array<struct {
allele_num: int32,
consequence_terms: array<str>,
high_inf_pos: str,
impact: str,
minimised: int32,
motif_feature_id: str,
motif_name: str,
motif_pos: int32,
motif_score_change: float64,
strand: int32,
variant_allele: str
}>,
regulatory_feature_consequences: array<struct {
allele_num: int32,
biotype: str,
consequence_terms: array<str>,
impact: str,
minimised: int32,
regulatory_feature_id: str,
variant_allele: str
}>,
seq_region_name: str,
start: int32,
strand: int32,
transcript_consequences: array<struct {
allele_num: int32,
amino_acids: str,
biotype: str,
canonical: int32,
ccds: str,
cdna_start: int32,
cdna_end: int32,
cds_end: int32,
cds_start: int32,
codons: str,
consequence_terms: array<str>,
distance: int32,
domains: array<struct {
db: str,
name: str
}>,
exon: str,
gene_id: str,
gene_pheno: int32,
gene_symbol: str,
gene_symbol_source: str,
hgnc_id: str,
hgvsc: str,
hgvsp: str,
hgvs_offset: int32,
impact: str,
intron: str,
lof: str,
lof_flags: str,
lof_filter: str,
lof_info: str,
minimised: int32,
polyphen_prediction: str,
polyphen_score: float64,
protein_end: int32,
protein_start: int32,
protein_id: str,
sift_prediction: str,
sift_score: float64,
strand: int32,
swissprot: str,
transcript_id: str,
trembl: str,
uniparc: str,
variant_allele: str
}>,
variant_class: str
}
'locus': locus<GRCh37>
'alleles': array<str>
'a_index': int32
'was_split': bool
'methylation': struct {
NUM: int32,
MEAN: float64,
GTE50: int32,
GTE60: int32,
GTE70: int32,
GTE80: int32,
GTE90: int32,
GTE100: int32
}
'coverage': struct {
exomes: struct {
row_id: int64,
mean: float64,
median: int32,
over_1: float64,
over_5: float64,
over_10: float64,
over_15: float64,
over_20: float64,
over_25: float64,
over_30: float64,
over_50: float64,
over_100: float64
},
genomes: struct {
row_id: int64,
mean: float64,
median: int32,
over_1: float64,
over_5: float64,
over_10: float64,
over_15: float64,
over_20: float64,
over_25: float64,
over_30: float64,
over_50: float64,
over_100: float64
}
}
'gerp': float64
'tx_annotation': array<struct {
ensg: str,
csq: str,
symbol: str,
lof: str,
lof_flag: str,
Cells_Transformedfibroblasts: float64,
Prostate: float64,
Spleen: float64,
Brain_FrontalCortex_BA9_: float64,
SmallIntestine_TerminalIleum: float64,
MinorSalivaryGland: float64,
Artery_Coronary: float64,
Skin_SunExposed_Lowerleg_: float64,
Cells_EBV_transformedlymphocytes: float64,
Brain_Hippocampus: float64,
Esophagus_Muscularis: float64,
Brain_Nucleusaccumbens_basalganglia_: float64,
Artery_Tibial: float64,
Brain_Hypothalamus: float64,
Adipose_Visceral_Omentum_: float64,
Cervix_Ectocervix: float64,
Brain_Spinalcord_cervicalc_1_: float64,
Brain_CerebellarHemisphere: float64,
Nerve_Tibial: float64,
Breast_MammaryTissue: float64,
Liver: float64,
Skin_NotSunExposed_Suprapubic_: float64,
AdrenalGland: float64,
Vagina: float64,
Pancreas: float64,
Lung: float64,
FallopianTube: float64,
Pituitary: float64,
Muscle_Skeletal: float64,
Colon_Transverse: float64,
Artery_Aorta: float64,
Heart_AtrialAppendage: float64,
Adipose_Subcutaneous: float64,
Esophagus_Mucosa: float64,
Heart_LeftVentricle: float64,
Brain_Cerebellum: float64,
Brain_Cortex: float64,
Thyroid: float64,
Brain_Substantianigra: float64,
Kidney_Cortex: float64,
Uterus: float64,
Stomach: float64,
WholeBlood: float64,
Bladder: float64,
Brain_Anteriorcingulatecortex_BA24_: float64,
Brain_Putamen_basalganglia_: float64,
Brain_Caudate_basalganglia_: float64,
Colon_Sigmoid: float64,
Cervix_Endocervix: float64,
Ovary: float64,
Esophagus_GastroesophagealJunction: float64,
Testis: float64,
Brain_Amygdala: float64,
mean_proportion: float64
}>
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Key: ['locus', 'alleles']
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