gnomad_genome_sites

  • Versions: 2.1.1, 3.1

  • Reference genome builds: GRCh37, GRCh38

  • Type: hail.Table

Schema (2.1.1, GRCh37)

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Global fields:
    'rf': struct {
        variants_by_type: dict<str, int32>,
        feature_medians: dict<str, struct {
            variant_type: str,
            n_alt_alleles: int32,
            qd: float64,
            pab_max: float64,
            info_MQRankSum: float64,
            info_SOR: float64,
            info_InbreedingCoeff: float64,
            info_ReadPosRankSum: float64,
            info_FS: float64,
            info_QD: float64,
            info_MQ: float64,
            info_DP: int32
        }>,
        test_intervals: array<interval<locus<GRCh37>>>,
        test_results: array<struct {
            rf_prediction: str,
            rf_label: str,
            n: int32
        }>,
        features_importance: dict<str, float64>,
        features: array<str>,
        vqsr_training: bool,
        no_transmitted_singletons: bool,
        adj: bool,
        rf_hash: str,
        rf_snv_cutoff: struct {
            bin: int32,
            min_score: float64
        },
        rf_indel_cutoff: struct {
            bin: int32,
            min_score: float64
        }
    }
    'freq_meta': array<dict<str, str>>
    'freq_index_dict': dict<str, int32>
    'popmax_index_dict': dict<str, int32>
    'age_index_dict': dict<str, int32>
    'faf_index_dict': dict<str, int32>
    'age_distribution': array<int32>
----------------------------------------
Row fields:
    'locus': locus<GRCh37>
    'alleles': array<str>
    'freq': array<struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32
    }>
    'age_hist_het': array<struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }>
    'age_hist_hom': array<struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }>
    'popmax': array<struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32,
        pop: str
    }>
    'faf': array<struct {
        meta: dict<str, str>,
        faf95: float64,
        faf99: float64
    }>
    'lcr': bool
    'decoy': bool
    'segdup': bool
    'nonpar': bool
    'variant_type': str
    'allele_type': str
    'n_alt_alleles': int32
    'was_mixed': bool
    'has_star': bool
    'qd': float64
    'pab_max': float64
    'info_MQRankSum': float64
    'info_SOR': float64
    'info_InbreedingCoeff': float64
    'info_ReadPosRankSum': float64
    'info_FS': float64
    'info_QD': float64
    'info_MQ': float64
    'info_DP': int32
    'transmitted_singleton': bool
    'fail_hard_filters': bool
    'info_POSITIVE_TRAIN_SITE': bool
    'info_NEGATIVE_TRAIN_SITE': bool
    'omni': bool
    'mills': bool
    'tp': bool
    'rf_train': bool
    'rf_label': str
    'rf_probability': float64
    'rank': int64
    'was_split': bool
    'singleton': bool
    '_score': float64
    '_singleton': bool
    'biallelic_rank': int64
    'singleton_rank': int64
    'n_nonref': int32
    'score': float64
    'adj_biallelic_singleton_rank': int64
    'adj_rank': int64
    'adj_biallelic_rank': int64
    'adj_singleton_rank': int64
    'biallelic_singleton_rank': int64
    'filters': set<str>
    'gq_hist_alt': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'gq_hist_all': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'dp_hist_alt': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'dp_hist_all': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'ab_hist_alt': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'qual': float64
    '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
    }
    'allele_info': struct {
        BaseQRankSum: float64,
        ClippingRankSum: float64,
        DB: bool,
        DP: int32,
        DS: bool,
        END: int32,
        FS: float64,
        HaplotypeScore: float64,
        InbreedingCoeff: float64,
        MQ: float64,
        MQ0: int32,
        MQRankSum: float64,
        NEGATIVE_TRAIN_SITE: bool,
        POSITIVE_TRAIN_SITE: bool,
        QD: float64,
        RAW_MQ: float64,
        ReadPosRankSum: float64,
        SOR: float64,
        VQSLOD: float64,
        culprit: str
    }
    'rsid': str
----------------------------------------
Key: ['locus', 'alleles']
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