TogoVar Downloadable data Last Updated: 2019/12/19 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_genotype_alt_alt :number of homozygous alternative genotypes in JGA-NGS jga_ngs_genotype_ref_alt :number of heterozygous genotypes in JGA-NGS jga_ngs_genotype_ref_ref :number of homozygous reference genotypes 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 3.5kjpn_allele_alt :number of alternative alleles in 3.5KJPNv1 3.5kjpn_allele_total :total number of alleles in 3.5KJPNv1 3.5kjpn_alt_allele_freq :alternative allele frequency in 3.5KJPNv1 3.5kjpn_genotype_alt_alt :number of homozygous alternative genotypes in 3.5KJPNv1 3.5kjpn_genotype_ref_alt :number of heterozygous genotypes in 3.5KJPNv1 3.5kjpn_genotype_ref_ref :number of homozygous reference genotypes in 3.5KJPNv1 3.5kjpn_qc_status :variant calling quality filter status for 3.5KJPNv1 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_genotype_alt_alt :number of homozygous alternative genotypes in HGVD hgvd_genotype_ref_alt :number of heterozygous genotypes in HGVD hgvd_genotype_ref_ref :number of homozygous reference genotypes in HGVD hgvd_qc_status :variant calling quality filter status for HGVD variant exac_total_allele_alt :total number of alternative alleles in the whole ExAC exac_total_allele_total :total number of alleles in the whole ExAC exac_total_alt_allele_freq :alternative allele frequency in the whole ExAC exac_total_genotype_alt_alt :number of homozygous alternative genotypes in the whole ExAC exac_total_genotype_ref_alt :number of heterozygous genotypes in the whole ExAC exac_total_genotype_ref_ref :number of homozygous reference genotypes in the whole ExAC exac_total_qc_status :variant calling quality filter status for ExAC variant exac_african_allele_alt :total number of alternative alleles in the African population of ExAC exac_african_allele_total :total number of alleles in the African population of ExAC exac_african_alt_allele_freq :alternative allele frequency in the African population of ExAC exac_african_genotype_alt_alt :number of homozygous alternative genotypes in the African population of ExAC exac_african_genotype_ref_alt :number of heterozygous genotypes in the African population of ExAC exac_african_genotype_ref_ref :number of homozygous reference genotypes in the African population of ExAC exac_eastasian_allele_alt :total number of alternative alleles in the East Asian population of ExAC exac_eastasian_allele_total :total number of alleles in the East Asian population of ExAC exac_eastasian_alt_allele_freq :alternative allele frequency in the East Asian population of ExAC exac_eastasian_genotype_alt_alt :number of homozygous alternative genotypes in the East Asian population of ExAC exac_eastasian_genotype_ref_alt :number of heterozygous genotypes in the East Asian population of ExAC exac_eastasian_genotype_ref_ref :number of homozygous reference genotypes in the East Asian population of ExAC exac_finnish_allele_alt :total number of alternative alleles in the Finnish population of ExAC exac_finnish_allele_total :total number of alleles in the Finnish population of ExAC exac_finnish_alt_allele_freq :alternative allele frequency in the Finnish population of ExAC exac_finnish_genotype_alt_alt :number of homozygous alternative genotypes in the Finnish population of ExAC exac_finnish_genotype_ref_alt :number of heterozygous genotypes in the Finnish population of ExAC exac_finnish_genotype_ref_ref :number of homozygous reference genotypes in the Finnish population of ExAC exac_european_allele_alt :total number of alternative alleles in the non-Finnish European population of ExAC exac_european_allele_total :total number of alleles in the non-Finnish European population of ExAC exac_european_alt_allele_freq :alternative allele frequency in the non-Finnish population of ExAC exac_european_genotype_alt_alt :number of homozygous alternative genotypes in the non-Finnish European population of ExAC exac_european_genotype_ref_alt :number of heterozygous genotypes in the non-Finnish European population of ExAC exac_european_genotype_ref_ref :number of homozygous reference genotypes in the non-Finnish European population of ExAC exac_latino_allele_alt :total number of alternative alleles in the Latino population of ExAC exac_latino_allele_total :total number of alleles in the Latino population of ExAC exac_latino_alt_allele_freq :alternative allele frequency in the Latino population of ExAC exac_latino_genotype_alt_alt :number of homozygous alternative genotypes in the Latino population of ExAC exac_latino_genotype_ref_alt :number of heterozygous genotypes in the Latino population of ExAC exac_latino_genotype_ref_ref :number of homozygous reference genotypes in the Latino population of ExAC exac_other_allele_alt :total number of alternative alleles in the Other population of ExAC exac_other_allele_total :total number of alleles in the Other population of ExAC exac_other_alt_allele_freq :alternative allele frequency in the Other population of ExAC exac_other_genotype_alt_alt :number of homozygous alternative genotypes in the Other population of ExAC exac_other_genotype_ref_alt :number of heterozygous genotypes in the Other population of ExAC exac_other_genotype_ref_ref :number of homozygous reference genotypes in the Other population of ExAC exac_southasian_allele_alt :total number of alternative alleles in the South Asian population of ExAC exac_southasian_allele_total :total number of alleles in the South Asian population of ExAC exac_southasian_alt_allele_freq :alternative allele frequency in the South Asian population of ExAC exac_southasian_genotype_alt_alt :number of homozygous alternative genotypes in the South Asian population of ExAC exac_southasian_genotype_ref_alt :number of heterozygous genotypes in the South Asian population of ExAC exac_southasian_genotype_ref_ref :number of homozygous reference genotypes in the South Asian population of ExAC 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