1000_genomes

  • Versions: phase3
  • Reference genome builds: GRCh37, GRCh38
  • Type: MatrixTable

Schema (phase3, GRCh37)

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Global fields:
    'metadata': struct {
        name: str,
        version: str,
        reference_genome: str,
        n_rows: int32,
        n_cols: int32,
        n_partitions: int32
    }
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Column fields:
    's': str
    'sex': str
    'super_population': str
    'population': str
    'sample_qc': struct {
        call_rate: float64,
        n_called: int64,
        n_not_called: int64,
        n_hom_ref: int64,
        n_het: int64,
        n_hom_var: int64,
        n_non_ref: int64,
        n_singleton: int64,
        n_snp: int64,
        n_insertion: int64,
        n_deletion: int64,
        n_transition: int64,
        n_transversion: int64,
        n_star: int64,
        r_ti_tv: float64,
        r_het_hom_var: float64,
        r_insertion_deletion: float64
    }
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Row fields:
    'locus': locus<GRCh37>
    'alleles': array<str>
    'rsid': str
    'qual': float64
    'filters': set<str>
    'info': struct {
        CIEND: int32,
        CIPOS: int32,
        CS: str,
        END: int32,
        IMPRECISE: bool,
        MC: array<str>,
        MEINFO: array<str>,
        MEND: int32,
        MLEN: int32,
        MSTART: int32,
        SVLEN: array<int32>,
        SVTYPE: str,
        TSD: str,
        AC: int32,
        AF: float64,
        NS: int32,
        AN: int32,
        EAS_AF: float64,
        EUR_AF: float64,
        AFR_AF: float64,
        AMR_AF: float64,
        SAS_AF: float64,
        DP: int32,
        AA: str,
        OLD_VARIANT: array<str>,
        VT: str,
        EX_TARGET: bool,
        MULTI_ALLELIC: bool
    }
    'was_split': bool
    'cm_position': float64
    'recombination_rate_cm_per_mb': float64
    'variant_qc': struct {
        AC: array<int32>,
        AF: array<float64>,
        AN: int32,
        homozygote_count: array<int32>,
        n_called: int64,
        n_not_called: int64,
        call_rate: float32,
        n_het: int64,
        n_non_ref: int64,
        het_freq_hwe: float64,
        p_value_hwe: float64
    }
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Entry fields:
    'GT': call
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Column key: ['s']
Row key: ['locus', 'alleles']
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