gnomad_plof_metrics_transcript

• Versions: 2.1.1

• Reference genome builds: GRCh37

• 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>
    'syn_sd': float64
    'mis_sd': float64
    'lof_sd': float64
----------------------------------------
Row fields:
    'gene': str
    'transcript': str
    'canonical': bool
    'obs_mis': int64
    'exp_mis': float64
    'oe_mis': float64
    'mu_mis': float64
    'possible_mis': int64
    'exp_mis_global': array<float64>
    'obs_mis_global': array<int64>
    'exp_mis_afr': array<float64>
    'obs_mis_afr': array<int64>
    'exp_mis_amr': array<float64>
    'obs_mis_amr': array<int64>
    'exp_mis_eas': array<float64>
    'obs_mis_eas': array<int64>
    'exp_mis_nfe': array<float64>
    'obs_mis_nfe': array<int64>
    'exp_mis_sas': array<float64>
    'obs_mis_sas': array<int64>
    'obs_mis_pphen': int64
    'exp_mis_pphen': float64
    'oe_mis_pphen': float64
    'possible_mis_pphen': int64
    'obs_syn': int64
    'exp_syn': float64
    'oe_syn': float64
    'mu_syn': float64
    'possible_syn': int64
    'exp_syn_global': array<float64>
    'obs_syn_global': array<int64>
    'exp_syn_afr': array<float64>
    'obs_syn_afr': array<int64>
    'exp_syn_amr': array<float64>
    'obs_syn_amr': array<int64>
    'exp_syn_eas': array<float64>
    'obs_syn_eas': array<int64>
    'exp_syn_nfe': array<float64>
    'obs_syn_nfe': array<int64>
    'exp_syn_sas': array<float64>
    'obs_syn_sas': array<int64>
    'obs_lof': int64
    'mu_lof': float64
    'possible_lof': int64
    'exp_lof': float64
    'exp_lof_global': array<float64>
    'obs_lof_global': array<int64>
    'exp_lof_afr': array<float64>
    'obs_lof_afr': array<int64>
    'exp_lof_amr': array<float64>
    'obs_lof_amr': array<int64>
    'exp_lof_eas': array<float64>
    'obs_lof_eas': array<int64>
    'exp_lof_nfe': array<float64>
    'obs_lof_nfe': array<int64>
    'exp_lof_sas': array<float64>
    'obs_lof_sas': array<int64>
    'pLI': float64
    'pNull': float64
    'pRec': float64
    'oe_lof': float64
    'oe_syn_lower': float64
    'oe_syn_upper': float64
    'oe_mis_lower': float64
    'oe_mis_upper': float64
    'oe_lof_lower': float64
    'oe_lof_upper': float64
    'constraint_flag': set<str>
    'syn_z': float64
    'mis_z': float64
    'lof_z': float64
    'oe_lof_upper_rank': int64
    'oe_lof_upper_bin': int32
    'oe_lof_upper_bin_6': int32
    'n_sites': int64
    'n_sites_array': array<int64>
    'classic_caf': float64
    'max_af': float64
    'classic_caf_array': array<float64>
    'no_lofs': int64
    'obs_het_lof': int64
    'obs_hom_lof': int64
    'defined': int64
    'pop_no_lofs': dict<str, int64>
    'pop_obs_het_lof': dict<str, int64>
    'pop_obs_hom_lof': dict<str, int64>
    'pop_defined': dict<str, int64>
    'p': float64
    'pop_p': dict<str, float64>
    'exp_hom_lof': float64
    'classic_caf_afr': float64
    'classic_caf_amr': float64
    'classic_caf_asj': float64
    'classic_caf_eas': float64
    'classic_caf_fin': float64
    'classic_caf_nfe': float64
    'classic_caf_oth': float64
    'classic_caf_sas': float64
    'p_afr': float64
    'p_amr': float64
    'p_asj': float64
    'p_eas': float64
    'p_fin': float64
    'p_nfe': float64
    'p_oth': float64
    'p_sas': float64
    'transcript_type': str
    'gene_id': str
    'transcript_level': str
    'cds_length': int64
    'num_coding_exons': int64
    'interval': interval<locus<GRCh37>>
    'gene_type': str
    'gene_length': int32
    'exac_pLI': float64
    'exac_obs_lof': int32
    'exac_exp_lof': float64
    'exac_oe_lof': float64
    'brain_expression': float64
----------------------------------------
Key: ['gene', 'transcript']
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