TogoVar Downloadable data Last Updated: 2021/12/16 See https://togovar.biosciencedbc.jp/doc/datasets about the datasets. -------------------------------------------- 1. Allele and genotype frequency Key value that identifies one record: tgv_id Variable name Description ------------------------------------------------------------------------------- tgv_id :Togovar ID rs :dbSNP rs number variant_type :variant type chr :chromosome number position_grch37 :chromosomal position on GRCh37 ref :reference allele alt :alternative allele symbol :HGNC gene symbol jga_ngs_allele_alt :number of alternative alleles in JGA-NGS jga_ngs_allele_total :total number of alleles in JGA-NGS jga_ngs_alt_allele_freq :alternative allele frequency in JGA-NGS jga_ngs_qc_status :variant calling quality filter status for JGA-NGS variant jga_snp_allele_alt :number of alternative alleles in JGA-SNP jga_snp_allele_total :total number of alleles in JGA-SNP jga_snp_alt_allele_freq :alternative allele frequency in JGA-SNP jga_snp_genotype_alt_alt :number of homozygous alternative genotypes in JGA-SNP jga_snp_genotype_ref_alt :number of heterozygous genotypes in JGA-SNP jga_snp_genotype_ref_ref :number of homozygous reference genotypes in JGA-SNP jga_snp_qc_status :variant calling quality filter status for JGA-SNP variant 8.3kjpn_allele_alt :number of alternative alleles in 8.3KJPN 8.3kjpn_allele_total :total number of alleles in 8.3KJPN 8.3kjpn_alt_allele_freq :alternative allele frequency in 8.3KJPN 8.3kjpn_qc_status :variant calling quality filter status for 8.3KJPN variant hgvd_allele_alt :number of alternative alleles in HGVD hgvd_allele_total :total number of alleles in HGVD hgvd_alt_allele_freq :alternative allele frequency in HGVD hgvd_qc_status :variant calling quality filter status for HGVD variant gem_j_wga_total_allele_alt :total number of alternative alleles in GEM-J WGA gem_j_wga_total_allele_total :total number of alleles in GEM-J WGA gem_j_wga_total_alt_allele_freq :alternative allele frequency in GEM-J WGA gem_j_wga_total_qc_status :variant calling quality filter status for GEM-J WGA variant gnomad_exomes_total_allele_alt :total number of alternative alleles in gnomAD exomes gnomad_exomes_total_allele_total :total number of alleles in gnomAD exomes gnomad_exomes_total_alt_allele_freq :alternative allele frequency in gnomAD exomes gnomad_exomes_total_qc_status :variant calling quality filter status for gnomAD exomes variant gnomad_genomes_total_allele_alt :total number of alternative alleles in gnomAD genomes gnomad_genomes_total_allele_total :total number of alleles in gnomAD genomes gnomad_genomes_total_alt_allele_freq :alternative allele frequency in gnomAD genomes gnomad_genomes_total_qc_status :variant calling quality filter status for gnomAD genomes variant 2. Molecular annotation Key values that identify one record: tgv_id and transcript_id Variable name Description --------------------------------------------------------------------- tgv_id :Togovar ID rs :dbSNP rs number chr :chromosome number position_grch37 :chromosomal position on GRCh37 position_grch38 :chromosomal position on GRCh38 ref :reference allele alt :alternative allele symbol :HGNC gene symbol transcript_id :Ensembl transcript ID consequence :molecular consequence predicted by Variant Effective Predictor sift_qualitative_prediction :qualitative prediction by SIFT sift_value :SIFT value polyphen2_qualitative_prediction :qualitative prediction by PolyPhen2 polyphen2_value :PolyPhen2 value