gnomad_genome_sites

  • Versions: 2.1.1, 3.1, 3.1.1, 3.1.2

  • Reference genome builds: GRCh37, GRCh38

  • Type: hail.Table

Schema (3.1.2, GRCh38)

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Global fields:
    'freq_meta': array<dict<str, str>>
    'freq_index_dict': dict<str, int32>
    'faf_index_dict': dict<str, int32>
    'faf_meta': array<dict<str, str>>
    'vep_version': str
    'vep_csq_header': str
    'dbsnp_version': str
    'filtering_model': struct {
        model_name: str,
        score_name: str,
        snv_cutoff: struct {
            bin: float64,
            min_score: float64
        },
        indel_cutoff: struct {
            bin: float64,
            min_score: float64
        },
        model_id: str,
        snv_training_variables: array<str>,
        indel_training_variables: array<str>
    }
    'age_distribution': struct {
        bin_edges: array<float64>,
        bin_freq: array<int32>,
        n_smaller: int32,
        n_larger: int32
    }
    'freq_sample_count': array<int32>
----------------------------------------
Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'freq': array<struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32
    }>
    'raw_qual_hists': struct {
        gq_hist_all: 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
        },
        gq_hist_alt: 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
        },
        ab_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        }
    }
    'popmax': struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32,
        pop: str,
        faf95: float64
    }
    'qual_hists': struct {
        gq_hist_all: 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
        },
        gq_hist_alt: 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
        },
        ab_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        }
    }
    'faf': array<struct {
        faf95: float64,
        faf99: float64
    }>
    'a_index': int32
    'was_split': bool
    'rsid': set<str>
    'filters': set<str>
    'info': struct {
        QUALapprox: int64,
        SB: array<int32>,
        MQ: float64,
        MQRankSum: float64,
        VarDP: int32,
        AS_ReadPosRankSum: float64,
        AS_pab_max: float64,
        AS_QD: float32,
        AS_MQ: float64,
        QD: float32,
        AS_MQRankSum: float64,
        FS: float64,
        AS_FS: float64,
        ReadPosRankSum: float64,
        AS_QUALapprox: int64,
        AS_SB_TABLE: array<int32>,
        AS_VarDP: int32,
        AS_SOR: float64,
        SOR: float64,
        singleton: bool,
        transmitted_singleton: bool,
        omni: bool,
        mills: bool,
        monoallelic: bool,
        AS_VQSLOD: float64,
        InbreedingCoeff: float64
    }
    'vep': struct {
        assembly_name: str,
        allele_string: str,
        ancestral: str,
        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,
            appris: 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,
            tsl: int32,
            uniparc: str,
            variant_allele: str
        }>,
        variant_class: str
    }
    'vqsr': struct {
        AS_VQSLOD: float64,
        AS_culprit: str,
        NEGATIVE_TRAIN_SITE: bool,
        POSITIVE_TRAIN_SITE: bool
    }
    'region_flag': struct {
        lcr: bool,
        segdup: bool
    }
    'allele_info': struct {
        variant_type: str,
        allele_type: str,
        n_alt_alleles: int32,
        was_mixed: bool
    }
    'age_hist_het': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'age_hist_hom': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'cadd': struct {
        phred: float32,
        raw_score: float32,
        has_duplicate: bool
    }
    'revel': struct {
        revel_score: float64,
        has_duplicate: bool
    }
    'splice_ai': struct {
        splice_ai_score: float32,
        splice_consequence: str,
        has_duplicate: bool
    }
    'primate_ai': struct {
        primate_ai_score: float32,
        has_duplicate: bool
    }
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Key: ['locus', 'alleles']
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