TogoVar datasets

Human genome reference sequence

Variant datasets derived from individual genome data in Japanese Genotype­-phenotype Archive (JGA)

Dataset name Version/Last update Sample size Number of detected variants Number of variants after the exclusion Author
JGA-NGS 06/01/2018 125 13,338,968 4,679,025 NBDC
JGA-SNP 06/01/2018 183,884 1,966,919 1,249,724 NBDC
Note that variants with 5 alternative alleles or less were excluded from JGA-NGS and JGA-SNP datasets.

Variant datasets generated by third parties

Dataset name Version/Last update Sample size Number of variants Number of variant sites Author
ClinVar 02/01/2017 — 198,707 — NCBI
Exome Aggregation Consortium (ExAC) Release 1 (02/27/2017) 60,706 10,195,872 9,362,319 Broad Institute
Human Genetic Variation Database (HGVD) Version 2.30 (08/02/2017) 1,208 554,461 501,556 Kyoto University
Integrative Japanese Genome Variation Database (iJGVD) 3.5KJPN (09/28/2017) 3,554 — 7,931,579 Tohoku Medical Megabank Organization
Note that of iJGVD 3.5KJPN variants, TogoVar contains only those accessible without DTA (i.e. their frequencies are 1% or more). See Data release for details.

Datasets other than those for variants

Dataset name Version/Last update Description Author
Colil 01/29/2018 Information on citation relationships in life sciences literature DBCLS
PubTator 04/23/2018 Information on papers in which the names of variants appear NCBI
TogoGenome hg19+UniProt_201804 Various information on genomes DBCLS