gnomad_hgdp_1kg_subset_sample_metadata
Versions: 3.1.2
Reference genome builds: GRCh38
Type:
hail.Table
Schema (3.1.2, GRCh38)
----------------------------------------
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
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<float64>,
bin_freq: array<int32>,
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<float64>,
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<str>,
hard_filtered: bool,
release_related: bool,
qc_metrics_filters: set<str>
}
'gnomad_high_quality': bool
'gnomad_release': bool
'relatedness_inference': struct {
related_samples: set<struct {
s: str,
kin: float64,
ibd0: float64,
ibd1: float64,
ibd2: float64
}>,
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<float64>,
subcontinental_pca: struct {
pca_scores: array<float64>,
pca_scores_outliers_removed: array<float64>,
outlier: bool
},
gnomad_labeled_subpop: str
}
'high_quality': bool
----------------------------------------
Key: ['s']
----------------------------------------