.. _gnomad_genome_sites: gnomad_genome_sites =================== * **Versions:** 2.1.1, 3.1, 3.1.1, 3.1.2 * **Reference genome builds:** GRCh37, GRCh38 * **Type:** :class:`hail.Table` Schema (3.1.2, GRCh38) ~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: text ---------------------------------------- Global fields: 'freq_meta': array> 'freq_index_dict': dict 'faf_index_dict': dict 'faf_meta': array> '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, indel_training_variables: array } 'age_distribution': struct { bin_edges: array, bin_freq: array, n_smaller: int32, n_larger: int32 } 'freq_sample_count': array ---------------------------------------- Row fields: 'locus': locus 'alleles': array 'freq': array 'raw_qual_hists': struct { gq_hist_all: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, dp_hist_all: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, gq_hist_alt: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, dp_hist_alt: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, ab_hist_alt: struct { bin_edges: array, bin_freq: array, 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, bin_freq: array, n_smaller: int64, n_larger: int64 }, dp_hist_all: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, gq_hist_alt: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, dp_hist_alt: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 }, ab_hist_alt: struct { bin_edges: array, bin_freq: array, n_smaller: int64, n_larger: int64 } } 'faf': array 'a_index': int32 'was_split': bool 'rsid': set 'filters': set 'info': struct { QUALapprox: int64, SB: array, 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, 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, impact: str, minimised: int32, variant_allele: str }>, most_severe_consequence: str, motif_feature_consequences: array, 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, impact: str, minimised: int32, regulatory_feature_id: str, variant_allele: str }>, seq_region_name: str, start: int32, strand: int32, transcript_consequences: array, distance: int32, domains: array, 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, bin_freq: array, n_smaller: int64, n_larger: int64 } 'age_hist_hom': struct { bin_edges: array, bin_freq: array, 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 } ---------------------------------------- Key: ['locus', 'alleles'] ----------------------------------------