gnomad_chrM_sites
Versions: 3.1
Reference genome builds: GRCh38
Type:
hail.Table
Schema (3.1, GRCh38)
----------------------------------------
Global fields:
'vep_version': str
'dbsnp_version': str
'hap_order': array<str>
'dp_hist_all_variants_bin_freq': array<int32>
'dp_hist_all_variants_n_larger': int32
'dp_hist_all_variants_bin_edges': array<float64>
'mq_hist_all_variants_bin_freq': array<int32>
'mq_hist_all_variants_n_larger': int32
'mq_hist_all_variants_bin_edges': array<float64>
'tlod_hist_all_variants_bin_freq': array<int32>
'tlod_hist_all_variants_n_larger': int32
'tlod_hist_all_variants_bin_edges': array<float64>
'age_hist_all_samples_bin_freq': array<int32>
'age_hist_all_samples_n_larger': int32
'age_hist_all_samples_n_smaller': int32
'age_hist_all_samples_bin_edges': array<float64>
'pop_order': array<str>
'global_annotation_descriptions': struct {
'vep_version': struct {
'Description': str
}
'dbsnp_version': struct {
'Description': str
}
'hap_order': struct {
'Description': str
}
'dp_hist_all_variants_bin_freq': struct {
'Description': str
}
'dp_hist_all_variants_n_larger': struct {
'Description': str
}
'dp_hist_all_variants_bin_edges': struct {
'Description': str
}
'mq_hist_all_variants_bin_freq': struct {
'Description': str
}
'mq_hist_all_variants_n_larger': struct {
'Description': str
}
'mq_hist_all_variants_bin_edges': struct {
'Description': str
}
'tlod_hist_all_variants_bin_freq': struct {
'Description': str
}
'tlod_hist_all_variants_n_larger': struct {
'Description': str
}
'tlod_hist_all_variants_bin_edges': struct {
'Description': str
}
'age_hist_all_samples_bin_freq': struct {
'Description': str
}
'age_hist_all_samples_n_larger': struct {
'Description': str
}
'age_hist_all_samples_n_smaller': struct {
'Description': str
}
'age_hist_all_samples_bin_edges': struct {
'Description': str
}
'pop_order': struct {
'Description': str
}
}
'row_annotation_descriptions': struct {
'locus': struct {
'Description': str
}
'alleles': struct {
'Description': str
}
'rsid': struct {
'Description': str
}
'filters': struct {
'Description': str
}
'variant_collapsed': struct {
'Description': str
}
'hap_defining_variant': struct {
'Description': str
}
'pon_mt_trna_prediction': struct {
'Description': str
}
'pon_ml_probability_of_pathogenicity': struct {
'Description': str
}
'mitotip_score': struct {
'Description': str
}
'mitotip_trna_prediction': struct {
'Description': str
}
'vep': struct {
'Description': str
}
'common_low_heteroplasmy': struct {
'Description': str
}
'base_qual_hist': struct {
'Description': str
}
'position_hist': struct {
'Description': str
}
'strand_bias_hist': struct {
'Description': str
}
'weak_evidence_hist': struct {
'Description': str
}
'contamination_hist': struct {
'Description': str
}
'heteroplasmy_below_min_het_threshold_hist': struct {
'Description': str
}
'excluded_AC': struct {
'Description': str
}
'AN': struct {
'Description': str
}
'AC_hom': struct {
'Description': str
}
'AC_het': struct {
'Description': str
}
'hl_hist': struct {
'Description': str
'sub_annotations': struct {
'bin_edges': struct {
'Description': str
}
'bin_freq': struct {
'Description': str
}
'n_smaller': struct {
'Description': str
}
'n_larger': struct {
'Description': str
}
}
}
'dp_hist_all': struct {
'Description': str
'sub_annotations': struct {
'bin_edges': struct {
'Description': str
}
'bin_freq': struct {
'Description': str
}
'n_smaller': struct {
'Description': str
}
'n_larger': struct {
'Description': str
}
}
}
'dp_hist_alt': struct {
'Description': str
'sub_annotations': struct {
'bin_edges': struct {
'Description': str
}
'bin_freq': struct {
'Description': str
}
'n_smaller': struct {
'Description': str
}
'n_larger': struct {
'Description': str
}
}
}
'dp_mean': struct {
'Description': str
}
'mq_mean': struct {
'Description': str
}
'tlod_mean': struct {
'Description': str
}
'AF_hom': struct {
'Description': str
}
'AF_het': struct {
'Description': str
}
'max_hl': struct {
'Description': str
}
'hap_AN': struct {
'Description': str
}
'hap_AC_het': struct {
'Description': str
}
'hap_AC_hom': struct {
'Description': str
}
'hap_AF_hom': struct {
'Description': str
}
'hap_AF_het': struct {
'Description': str
}
'hap_hl_hist': struct {
'Description': str
}
'hap_faf_hom': struct {
'Description': str
}
'hapmax_AF_hom': struct {
'Description': str
}
'hapmax_AF_het': struct {
'Description': str
}
'faf_hapmax_hom': struct {
'Description': str
}
'pop_AN': struct {
'Description': str
}
'pop_AC_het': struct {
'Description': str
}
'pop_AC_hom': struct {
'Description': str
}
'pop_AF_hom': struct {
'Description': str
}
'pop_AF_het': struct {
'Description': str
}
'pop_hl_hist': struct {
'Description': str
}
'age_hist_hom': struct {
'Description': str
'sub_annotations': struct {
'bin_edges': struct {
'Description': str
}
'bin_freq': struct {
'Description': str
}
'n_smaller': struct {
'Description': str
}
'n_larger': struct {
'Description': str
}
}
}
'age_hist_het': struct {
'Description': str
'sub_annotations': struct {
'bin_edges': struct {
'Description': str
}
'bin_freq': struct {
'Description': str
}
'n_smaller': struct {
'Description': str
}
'n_larger': struct {
'Description': str
}
}
}
}
----------------------------------------
Row fields:
'locus': locus<GRCh38>
'alleles': array<str>
'filters': set<str>
'variant_collapsed': str
'hap_defining_variant': bool
'pon_mt_trna_prediction': str
'pon_ml_probability_of_pathogenicity': float64
'mitotip_score': float64
'mitotip_trna_prediction': str
'vep': struct {
assembly_name: str,
allele_string: str,
ancestral: str,
colocated_variants: array<struct {
aa_allele: str,
aa_maf: float64,
afr_allele: str,
afr_maf: float64,
allele_string: str,
amr_allele: str,
amr_maf: float64,
clin_sig: array<str>,
end: int32,
eas_allele: str,
eas_maf: float64,
ea_allele: str,
ea_maf: float64,
eur_allele: str,
eur_maf: float64,
exac_adj_allele: str,
exac_adj_maf: float64,
exac_allele: str,
exac_afr_allele: str,
exac_afr_maf: float64,
exac_amr_allele: str,
exac_amr_maf: float64,
exac_eas_allele: str,
exac_eas_maf: float64,
exac_fin_allele: str,
exac_fin_maf: float64,
exac_maf: float64,
exac_nfe_allele: str,
exac_nfe_maf: float64,
exac_oth_allele: str,
exac_oth_maf: float64,
exac_sas_allele: str,
exac_sas_maf: float64,
id: str,
minor_allele: str,
minor_allele_freq: float64,
phenotype_or_disease: int32,
pubmed: array<int32>,
sas_allele: str,
sas_maf: float64,
somatic: int32,
start: int32,
strand: int32
}>,
context: str,
end: int32,
id: str,
input: str,
intergenic_consequences: array<struct {
allele_num: int32,
consequence_terms: array<str>,
impact: str,
minimised: int32,
variant_allele: str
}>,
most_severe_consequence: str,
motif_feature_consequences: array<struct {
allele_num: int32,
consequence_terms: array<str>,
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<struct {
allele_num: int32,
biotype: str,
consequence_terms: array<str>,
impact: str,
minimised: int32,
regulatory_feature_id: str,
variant_allele: str
}>,
seq_region_name: str,
start: int32,
strand: int32,
transcript_consequences: array<struct {
allele_num: int32,
amino_acids: str,
appris: str,
biotype: str,
canonical: int32,
ccds: str,
cdna_start: int32,
cdna_end: int32,
cds_end: int32,
cds_start: int32,
codons: str,
consequence_terms: array<str>,
distance: int32,
domains: array<struct {
db: str,
name: str
}>,
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
}
'rsid': set<str>
'common_low_heteroplasmy': bool
'base_qual_hist': array<int64>
'position_hist': array<int64>
'strand_bias_hist': array<int64>
'weak_evidence_hist': array<int64>
'contamination_hist': array<int64>
'heteroplasmy_below_min_het_threshold_hist': array<int64>
'excluded_AC': int64
'AN': int64
'AC_hom': int64
'AC_het': int64
'hl_hist': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'dp_hist_all': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'dp_hist_alt': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'dp_mean': float64
'mq_mean': float64
'tlod_mean': float64
'AF_hom': float32
'AF_het': float32
'max_hl': float64
'hap_AN': array<int64>
'hap_AC_het': array<int64>
'hap_AC_hom': array<int64>
'hap_AF_hom': array<float32>
'hap_AF_het': array<float32>
'hap_hl_hist': array<array<int64>>
'hap_faf_hom': array<float64>
'hapmax_AF_hom': str
'hapmax_AF_het': str
'faf_hapmax_hom': float64
'pop_AN': array<int64>
'pop_AC_het': array<int64>
'pop_AC_hom': array<int64>
'pop_AF_hom': array<float32>
'pop_AF_het': array<float32>
'pop_hl_hist': array<array<int64>>
'age_hist_hom': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'age_hist_het': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
----------------------------------------
Key: ['locus', 'alleles']
----------------------------------------