resource_id	resource_type	browser_track	download_file	file_name	download_url	content	source_cohort	processing_stage	reference_assembly	filters_applied	counting_unit	pipeline_version	coordinate_derivation	data_provenance	dbsnp_build_for_rsid	record_count	record_count_unit	record_count_detail	file_size_bytes	md5	footnotes
HGVD-v3.1-01	browser_track	Gene					Gene models with NCBI cross-references	Imported browser annotation	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Not applicable	Not applicable	Not applicable (imported annotation)	Imported assembly-specific annotation	NCBI Gene annotation							
HGVD-v3.1-02	browser_track	dbSNP					NCBI dbSNP variants	Imported variant annotation	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Not applicable	Not applicable	Not applicable (imported annotation)	Imported assembly-specific annotation	NCBI dbSNP annotation							
HGVD-v3.1-03	browser_track_and_file	Exome; allele frequency, samples covered, and average read depth	HGVD Release Version 3.1 (GRCh37/hg19): HGVD-V3_10-dbSNP151.tar.gz	HGVD-V3_10-dbSNP151.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD-V3_10-dbSNP151.tar.gz	Autosomes (chr1-chr22)	Exome dataset (n = 1,209)	Aggregate browser summaries generated from the final released GRCh37/hg19 exome call set; GRCh38/hg38 and T2T-CHM13 browser views generated by liftOver	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Sample and variant QC with VQSR-filtered calls, as described in Methods	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	Picard/GATK v3.8 Best Practices reprocessing (HaplotypeCaller, joint genotyping, VQSR); see Methods	GRCh37/hg19 native release coordinates; GRCh38/hg38 and T2T-CHM13 derived by UCSC liftOver from GRCh37/hg19	HGVD exome aggregate genotype and allele counts	dbSNP Build151				1249129953	be40bd8c0f4b471c3e9d276f6bc32b8a	a,b,c,d
HGVD-v3.1-04	browser_track_and_file	Exome; allele frequency, samples covered, and average read depth	HGVD Release Version 3.1 (GRCh37/hg19): HGVD-V3_10XY-dbSNP151.tar.gz	HGVD-V3_10XY-dbSNP151.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD-V3_10XY-dbSNP151.tar.gz	Sex chromosomes (chrX, chrY)	Exome dataset (n = 1,209)	Aggregate browser summaries generated from the final released GRCh37/hg19 exome call set; GRCh38/hg38 and T2T-CHM13 browser views generated by liftOver	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Sample and variant QC with VQSR-filtered calls, as described in Methods	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	Picard/GATK v3.8 Best Practices reprocessing (HaplotypeCaller, joint genotyping, VQSR); see Methods	GRCh37/hg19 native release coordinates; GRCh38/hg38 and T2T-CHM13 derived by UCSC liftOver from GRCh37/hg19	HGVD exome aggregate genotype and allele counts	dbSNP Build151				49421633	97234d0a04ff7c4c5591994c3d449f69	a,b,c,d
HGVD-v3.1-05	browser_track_and_file	WGS; allele frequency, samples covered, and average read depth	HGVD Release Version 3.1 (GRCh37/hg19): HGVD-V3_10-dbSNP151.tar.gz	HGVD-V3_10-dbSNP151.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD-V3_10-dbSNP151.tar.gz	Autosomes (chr1-chr22)	WGS dataset (n = 3,135)	Aggregate browser summaries generated from the final released GRCh37/hg19 WGS call set; GRCh38/hg38 and T2T-CHM13 browser views generated by liftOver	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Sample and variant QC with VQSR-filtered calls, as described in Methods and reference (4)	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	BWA-MEM alignment; Picard/GATK v3.8 Best Practices (duplicate marking, base-quality recalibration, HaplotypeCaller, joint genotyping, VQSR)	GRCh37/hg19 native release coordinates; GRCh38/hg38 and T2T-CHM13 derived by UCSC liftOver from GRCh37/hg19	HGVD WGS aggregate genotype and allele counts	dbSNP Build151				1249129953	be40bd8c0f4b471c3e9d276f6bc32b8a	a,b,c,d
HGVD-v3.1-06	browser_track_and_file	WGS; allele frequency, samples covered, and average read depth	HGVD Release Version 3.1 (GRCh37/hg19): HGVD-V3_10XY-dbSNP151.tar.gz	HGVD-V3_10XY-dbSNP151.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD-V3_10XY-dbSNP151.tar.gz	Sex chromosomes (chrX, chrY)	WGS dataset (n = 3,135)	Aggregate browser summaries generated from the final released GRCh37/hg19 WGS call set; GRCh38/hg38 and T2T-CHM13 browser views generated by liftOver	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	Sample and variant QC with VQSR-filtered calls, as described in Methods and reference (4)	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	BWA-MEM alignment; Picard/GATK v3.8 Best Practices (duplicate marking, base-quality recalibration, HaplotypeCaller, joint genotyping, VQSR)	GRCh37/hg19 native release coordinates; GRCh38/hg38 and T2T-CHM13 derived by UCSC liftOver from GRCh37/hg19	HGVD WGS aggregate genotype and allele counts	dbSNP Build151				49421633	97234d0a04ff7c4c5591994c3d449f69	a,b,c,d
HGVD-v3.1-07	browser_track	Genotyping; allele frequency and samples covered					SNP array dataset (n = 3,248)	Aggregate browser summaries generated from the final released GRCh37/hg19 SNP-array genotype dataset; GRCh38/hg38 and T2T-CHM13 browser views generated by liftOver	GRCh37/hg19, GRCh38/hg38, and T2T-CHM13	SNP-array marker and sample QC described in references (10, 11)	Per-locus genotype and allele counts, successfully genotyped sample count, and missing-genotype handling.	iScan Control Software (ICS) for scanning and GenomeStudio for genotyping analysis	GRCh37/hg19 source coordinates; GRCh38/hg38 and T2T-CHM13 browser views derived by liftOver	Final Report from GenomeStudio							b,c
HGVD-v3.1-08	browser_track_and_file	eQTL	HGVD eQTL Release Version 8.1: HGVDeQTL-V8_1-cis.tar.gz	HGVDeQTL-V8_1-cis.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/eQTL/version.8.1/HGVDeQTL-V8_1-cis.tar.gz		eQTL panel (n = 300)	Published eQTL association results incorporated into HGVD	GRCh37/hg19	Association-analysis criteria described in reference (9)	Variant–probe association record; allele-count, genotype-count and callable-sample denominators not reported	Published eQTL analysis pipeline (reference 9); incorporated into HGVD without hg38/T2T reprocessing	Native GRCh37/hg19 coordinates; no hg38/T2T eQTL track	Published eQTL association statistics (reference 9)	Not applicable				456703313	4f798100f571418d2fee934391aa12f4	
HGVD-v3.1-09	download_file	Not applicable	HGVD Structural Variants Version 1.0 (GRCh37/hg19): HGVD_SV-V1_00.vcf.gz	HGVD_SV-V1_00.vcf.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD_SV-V1_00.vcf.gz		WGS dataset and Seven Bridges graph-genome source records	Integrated structural-variant VCF release	GRCh37/hg19	WGS dataset: Manta-based SV calling, cross-sample merging, bcftools normalization, and filtering described in reference (4); Seven Bridges records: source-resource criteria	VCF record and alternate allele; aggregate AC and AN are provided for records from the WGS dataset	Manta-based SV calling; cross-sample merging; bcftools normalization (Methods; reference 4)	Native GRCh37/hg19 coordinates	HGVD WGS aggregate AC/AN and source-derived external frequency annotations	Not applicable	16112052	VCF records	Integrated release: 16,112,052 records / 17,491,876 alternate alleles. Of these, 438,056 records are HGVD-derived and carry aggregate AC and AN from the WGS cohort; 15,847,592 records (17,069,591 alternate alleles) are imported from the Seven Bridges graph-genome source and carry no HGVD genotypes. The two counts do not sum to the integrated total because records describing the same structural allele were merged (Table 2).	1058303960	79051eef01fbb8223efbe347c0413c48	
HGVD-v3.1-10	download_file	Not applicable	HGVD Release Version 2.30: HGVD1210-V2_30-dbSNP150.tar.gz	HGVD1210-V2_30-dbSNP150.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD1210-V2_30-dbSNP150.tar.gz	Autosomes (chr1-chr22)	Legacy HGVD exome cohort (n = 1,210)	Legacy HGVD Release Version 2.30 retained on the Download page	GRCh37/hg19	Centre-specific variant-calling filters described in reference (5); per-locus filter status reported in the downloadable table	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	Legacy centre-specific exome calling pipelines (reference 5; Version 2.30 release documentation)	Native GRCh37/hg19 coordinates	Legacy HGVD exome aggregate genotype and allele counts	dbSNP Build150 (legacy Version 2.30, unchanged)				11761401	f72ef4099260c832d38c49f0ca60017f	a
HGVD-v3.1-11	download_file	Not applicable	HGVD Release Version 2.30: HGVD1210-V2_30XY-dbSNP150.tar.gz	HGVD1210-V2_30XY-dbSNP150.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/HGVD1210-V2_30XY-dbSNP150.tar.gz	Sex chromosomes (chrX, chrY)	Legacy HGVD exome cohort (n = 1,210)	Legacy HGVD Release Version 2.30 retained on the Download page	GRCh37/hg19	Centre-specific variant-calling filters described in reference (5); per-locus filter status reported in the downloadable table	Per-locus genotype, allele, and sample counts (RR, RA, AA, NR, NA and #Sample)	Legacy centre-specific exome calling pipelines (reference 5; Version 2.30 release documentation)	Native GRCh37/hg19 coordinates	Legacy HGVD exome aggregate genotype and allele counts	dbSNP Build150 (legacy Version 2.30, unchanged)				313669	15d1750c7c51fa90697d098956676836	a
HGVD-v3.1-12	download_file	Not applicable	HGVD Japanese Reference Sequence Version 1.0 (GRCh37/hg19): JapaneseReferenceV1.0.tar.gz	JapaneseReferenceV1.0.tar.gz	https://www.hgvd.genome.med.kyoto-u.ac.jp/download/JapaneseReferenceV1.0.tar.gz		HGVD Japanese Reference Sequence Version 1.0	Legacy Japanese Reference Sequence Version 1.0 retained on the Download page	GRCh37/hg19	Not applicable (reference-sequence resource)	Not applicable	Not applicable (reference-sequence resource)	Native GRCh37/hg19 coordinates	HGVD Japanese Reference Sequence Version 1.0	Not applicable				937520108	24c13c1d20efa45c58c8f05f6fa40427	
HGVD-v3.1-13	browser_track_and_file	pathSTR (locus report pages)	pathSTR locus reports (HTML, one per locus)		https://www.hgvd.genome.med.kyoto-u.ac.jp/pathstr.html		1000 Genomes Project Oxford Nanopore dataset (n = 1,019)	Per-locus tandem-repeat length and motif distributions generated with STRdust and rendered with aSTRonaut	T2T-CHM13	STRdust consensus-read filtering and outlier detection; see Methods and Supplementary Tables S4 and S5	Repeat-allele length and motif composition per locus; no HGVD allele or genotype counts are reported	STRdust v1; aSTRonaut (pathSTR)	Native T2T-CHM13 coordinates (T2T.STRchive-disease-loci.TRGT.bed)	Derived from the 1000 Genomes ONT cohort, not from HGVD samples; locus mapping in Supplementary Table S3 and locus-level QC in Supplementary Table S4	Not applicable	68	Loci	68 BED-defined loci (Supplementary Table S3)