.. _gnomad_hgdp_1kg_subset_sample_metadata: gnomad_hgdp_1kg_subset_sample_metadata ====================================== * **Versions:** 3.1.2 * **Reference genome builds:** GRCh38 * **Type:** :class:`hail.Table` Schema (3.1.2, GRCh38) ~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: text ---------------------------------------- Global fields: 'global_annotation_descriptions': struct { gnomad_sex_imputation_ploidy_cutoffs: struct { Description: str }, gnomad_population_inference_pca_metrics: struct { Description: str }, sample_hard_filter_cutoffs: struct { Description: str }, gnomad_sample_qc_metric_outlier_cutoffs: struct { Description: str }, gnomad_age_distribution: struct { Description: str, sub_globals: struct { bin_edges: struct { Description: str }, bin_freq: struct { Description: str }, n_smaller: struct { Description: str }, n_larger: struct { Description: str } } } } 'sample_annotation_descriptions': struct { s: struct { Description: str }, bam_metrics: struct { Description: str, sub_annotations: struct { pct_bases_20x: struct { Description: str }, pct_chimeras: struct { Description: str }, freemix: struct { Description: str }, mean_coverage: struct { Description: str }, median_coverage: struct { Description: str }, mean_insert_size: struct { Description: str }, median_insert_size: struct { Description: str }, pct_bases_10x: struct { Description: str } } }, sample_qc: struct { Description: str, sub_annotations: struct { n_deletion: struct { Description: str }, n_het: struct { Description: str }, n_hom_ref: struct { Description: str }, n_hom_var: struct { Description: str }, n_insertion: struct { Description: str }, n_non_ref: struct { Description: str }, n_snp: struct { Description: str }, n_transition: struct { Description: str }, n_transversion: struct { Description: str }, r_het_hom_var: struct { Description: str }, r_insertion_deletion: struct { Description: str }, r_ti_tv: struct { Description: str } } }, gnomad_sex_imputation: struct { Description: str, sub_annotations: struct { chr20_mean_dp: struct { Description: str }, chrX_mean_dp: struct { Description: str }, chrY_mean_dp: struct { Description: str }, chrX_ploidy: struct { Description: str }, chrY_ploidy: struct { Description: str }, X_karyotype: struct { Description: str }, Y_karyotype: struct { Description: str }, sex_karyotype: struct { Description: str }, f_stat: struct { Description: str }, n_called: struct { Description: str }, expected_homs: struct { Description: str }, observed_homs: struct { Description: str } } }, gnomad_population_inference: struct { Description: str, sub_annotations: struct { pca_scores: struct { Description: str }, pop: struct { Description: str }, prob_afr: struct { Description: str }, prob_ami: struct { Description: str }, prob_amr: struct { Description: str }, prob_asj: struct { Description: str }, prob_eas: struct { Description: str }, prob_fin: struct { Description: str }, prob_mid: struct { Description: str }, prob_nfe: struct { Description: str }, prob_oth: struct { Description: str }, prob_sas: struct { Description: str } } }, gnomad_sample_qc_residuals: struct { Description: tuple ( str ), sub_annotations: struct { n_snp_residual: struct { Description: str }, r_ti_tv_residual: struct { Description: str }, r_insertion_deletion_residual: struct { Description: str }, n_insertion_residual: struct { Description: str }, n_deletion_residual: struct { Description: str }, r_het_hom_var_residual: struct { Description: str }, n_transition_residual: struct { Description: str }, n_transversion_residual: struct { Description: str } } }, gnomad_sample_filters: struct { Description: str, sub_annotations: struct { hard_filters: struct { Description: str }, hard_filtered: struct { Description: str }, release_related: struct { Description: str }, qc_metrics_filters: struct { Description: str } } }, gnomad_high_quality: struct { Description: str }, gnomad_release: struct { Description: str }, relatedness_inference: struct { Description: str, sub_annotations: struct { related_samples: struct { Description: str, sub_annotations: struct { s: struct { Description: str }, kin: struct { Description: str }, ibd0: struct { Description: str }, ibd1: struct { Description: str }, ibd2: struct { Description: str } } }, related: struct { Description: str } } }, hgdp_tgp_meta: struct { Description: str, sub_annotations: struct { project: struct { Description: str }, study_region: struct { Description: str }, population: struct { Description: str }, genetic_region: struct { Description: str }, latitude: struct { Description: str }, longitude: struct { Description: str }, hgdp_technical_meta: struct { Description: str, sub_annotations: struct { source: struct { Description: str }, library_type: struct { Description: str } } }, global_pca_scores: struct { Description: str }, subcontinental_pca: struct { Description: str, sub_annotations: struct { pca_scores: struct { Description: str }, pca_scores_outliers_removed: struct { Description: str }, outlier: struct { Description: str } } }, gnomad_labeled_subpop: struct { Description: str } } }, high_quality: struct { Description: str } } 'gnomad_sex_imputation_ploidy_cutoffs': struct { x_ploidy_cutoffs: struct { upper_cutoff_X: float64, lower_cutoff_XX: float64, upper_cutoff_XX: float64, lower_cutoff_XXX: float64 }, y_ploidy_cutoffs: struct { lower_cutoff_Y: float64, upper_cutoff_Y: float64, lower_cutoff_YY: float64 }, f_stat_cutoff: float64 } 'gnomad_population_inference_pca_metrics': struct { n_pcs: int32, min_prob: float64 } 'sample_hard_filter_cutoffs': struct { min_cov: int32, max_n_snp: float64, min_n_snp: float64, max_n_singleton: float64, max_r_het_hom_var: float64, max_pct_contamination: float64, max_pct_chimera: float64, min_median_insert_size: int32 } 'gnomad_sample_qc_metric_outlier_cutoffs': struct { lms: struct { n_snp: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, n_singleton: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, r_ti_tv: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, r_insertion_deletion: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, n_insertion: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, n_deletion: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, r_het_hom_var: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, n_transition: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 }, n_transversion: struct { beta: array, standard_error: array, t_stat: array, p_value: array, multiple_standard_error: float64, multiple_r_squared: float64, adjusted_r_squared: float64, f_stat: float64, multiple_p_value: float64, n: int32 } }, qc_metrics_stats: struct { n_snp_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, n_singleton_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, r_ti_tv_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, r_insertion_deletion_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, n_insertion_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, n_deletion_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, r_het_hom_var_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, n_transition_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 }, n_transversion_residual: struct { median: float64, mad: float64, lower: float64, upper: float64 } }, n_pcs: int32, used_regressed_metrics: bool } 'gnomad_age_distribution': struct { bin_edges: array, bin_freq: array, n_smaller: int32, n_larger: int32 } ---------------------------------------- Row fields: 's': str 'bam_metrics': struct { pct_bases_20x: float64, pct_chimeras: float64, freemix: float64, mean_coverage: float64, median_coverage: float64, mean_insert_size: float64, median_insert_size: float64, pct_bases_10x: float64 } 'sample_qc': struct { n_deletion: int64, n_het: int64, n_hom_ref: int64, n_hom_var: int64, n_insertion: int64, n_non_ref: int64, n_snp: int64, n_transition: int64, n_transversion: int64, r_het_hom_var: float64, r_insertion_deletion: float64, r_ti_tv: float64 } 'gnomad_sex_imputation': struct { chr20_mean_dp: float32, chrX_mean_dp: float32, chrY_mean_dp: float32, chrX_ploidy: float32, chrY_ploidy: float32, X_karyotype: str, Y_karyotype: str, sex_karyotype: str, f_stat: float64, n_called: int64, expected_homs: float64, observed_homs: int64 } 'gnomad_population_inference': struct { pca_scores: array, pop: str, prob_afr: float64, prob_ami: float64, prob_amr: float64, prob_asj: float64, prob_eas: float64, prob_fin: float64, prob_mid: float64, prob_nfe: float64, prob_oth: float64, prob_sas: float64 } 'gnomad_sample_qc_residuals': struct { n_snp_residual: float64, r_ti_tv_residual: float64, r_insertion_deletion_residual: float64, n_insertion_residual: float64, n_deletion_residual: float64, r_het_hom_var_residual: float64, n_transition_residual: float64, n_transversion_residual: float64 } 'gnomad_sample_filters': struct { hard_filters: set, hard_filtered: bool, release_related: bool, qc_metrics_filters: set } 'gnomad_high_quality': bool 'gnomad_release': bool 'relatedness_inference': struct { related_samples: set, related: bool } 'hgdp_tgp_meta': struct { project: str, study_region: str, population: str, genetic_region: str, latitude: float64, longitude: float64, hgdp_technical_meta: struct { source: str, library_type: str }, global_pca_scores: array, subcontinental_pca: struct { pca_scores: array, pca_scores_outliers_removed: array, outlier: bool }, gnomad_labeled_subpop: str } 'high_quality': bool ---------------------------------------- Key: ['s'] ----------------------------------------