1.2. Datasets included in jMorp

At the time of writing, the following datasets are present in jMorp.

  • Genome Sequnece

    • JG 2.1.0: Japanese reference sequence constructed from de-novo assembly of 3 Japanese males (Takayama et al. [1])

  • Genome Variation

    • 38KJPN: SNV/INDEL allele and genotype frequency data derived from the short-read whole genome sequencing of over 38,000 Japanese individuals (Tadaka et al. [2])

    • 38KJPN-HLA: HLA allele frequency data derived from the short-read whole genome sequencing of over 38,000 Japanese individuals

    • 8.3KJPN-SV: Allele and genotype frequency data of structural variations (SVs) derived from the short-read whole genome sequencing of more than 8,300 Japanese individuals

    • JSV1: Allele and genotype frequency data of SVs derived from the long-read whole genome sequencing of 222 Japanese individuals (Otsuki et al. [3])

  • Genome (others)

    • Genome Accessibility: Average depth information from short-read WGS

    • Genetic Map: linkage disequilibrium map derived from 300 haploids

    • Japonica Array marker list: lists of markers tiled on Japonica Arrays (SNP Arrays) developed by ToMMo (Sakurai-Yageta et al. [4], Fuse et al. [5])

  • Methylome

    • IMM 3cell analysis: data on DNA methylation, gene expression, and allele frequency for three different blood cell types in approximately 100 Japanese individuals (Hachiya et al. [6], Komaki et al. [7])

  • Transcriptome

    • ToMMo ISO-Seq: long-read transcriptome analysis of three Japanese male individuals (Otsuki et al. [8])

    • IMM 3cell analysis: data on DNA methylation, gene expression, and allele frequency for three different blood cell types in approximately 100 Japanese individuals (Hachiya et al. [6], Komaki et al. [7])

  • Proteome

    • Proteome: proteome analysis of about 500 Japanese plasma samples (Koshiba et al. [9], Saigusa et al. [10])

  • Metabolome

    • Metabolome: Metabolome analysis results obtained from around 53,000 Japanese plasma samples (Koshiba et al. [9], Saigusa et al. [10], Saigusa et al. [11])

  • Phenome

    • PGx: drug sensitivity-related enzymes’ genome variants and enzyme activity

    • Metagenome 16S-v4 (2021): microbiome analysis of plaque and saliva samples (16S v4 region analysis) (Saito et al. [12])

    • Metagenome 16S-v3/v4 (2023): Microbiome analysis of plaque and saliva samples (16S v3/v4 region analysis)

  • Other

    • GWAS: a repository for the TMM project’s GWAS analysis results

The data included in jMorp are listed above, arranged according to the hierarchy of the Central Dogma. The jMorp is a multi-omics database, and it contains data from all layers of the Central Dogma can be found in jMorp. Using jMorp, it is easy to get a broad picture of the diversity of the Japanese population across many layers of genome-omics data.

To learn more about each dataset, see Details of datasets included in jMorp.