gnomad_chrM_sites

  • Versions: 3.1

  • Reference genome builds: GRCh38

  • Type: hail.Table

Schema (3.1, GRCh38)

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Global fields:
    'vep_version': str
    'dbsnp_version': str
    'hap_order': array<str>
    'dp_hist_all_variants_bin_freq': array<int32>
    'dp_hist_all_variants_n_larger': int32
    'dp_hist_all_variants_bin_edges': array<float64>
    'mq_hist_all_variants_bin_freq': array<int32>
    'mq_hist_all_variants_n_larger': int32
    'mq_hist_all_variants_bin_edges': array<float64>
    'tlod_hist_all_variants_bin_freq': array<int32>
    'tlod_hist_all_variants_n_larger': int32
    'tlod_hist_all_variants_bin_edges': array<float64>
    'age_hist_all_samples_bin_freq': array<int32>
    'age_hist_all_samples_n_larger': int32
    'age_hist_all_samples_n_smaller': int32
    'age_hist_all_samples_bin_edges': array<float64>
----------------------------------------
Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'rsid': str
    'qual': float64
    'filters': set<str>
    'variant_collapsed': str
    'hap_defining_variant': bool
    'pon_mt_trna_prediction': str
    'pon_ml_probability_of_pathogenicity': float64
    'mitotip_score': float64
    'mitotip_trna_prediction': 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,
            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
    }
    'common_low_heteroplasmy': bool
    'base_qual_hist': array<int64>
    'position_hist': array<int64>
    'strand_bias_hist': array<int64>
    'weak_evidence_hist': array<int64>
    'contamination_hist': array<int64>
    'heteroplasmy_below_10_percent_hist': array<int64>
    'excluded_AC': int64
    'AN': int64
    'AC_hom': int64
    'AC_het': int64
    'hl_hist': 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
    }
    'dp_hist_alt': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'dp_mean': float64
    'mq_mean': float64
    'tlod_mean': float64
    'AF_hom': float32
    'AF_het': float32
    'max_hl': float64
    'hap_AN': array<int64>
    'hap_AC_het': array<int64>
    'hap_AC_hom': array<int64>
    'hap_AF_hom': array<float32>
    'hap_AF_het': array<float32>
    'hap_hl_hist': array<array<int64>>
    'hap_faf_hom': array<float64>
    'hapmax_AF_hom': str
    'hapmax_AF_het': str
    'faf_hapmax_hom': float64
    'age_hist_hom': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
    'age_hist_het': struct {
        bin_edges: array<float64>,
        bin_freq: array<int64>,
        n_smaller: int64,
        n_larger: int64
    }
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Key: ['locus', 'alleles']
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