1.2. Datasets included in jMorp

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

• Genome Sequnece

  • JG 3.0.0: Japanese reference sequence constructed from de-novo assembly of 3 Japanese males (Takayama et al. [1])

• Genome Variation

  • 61KJPN: SNV/INDEL allele frequency and genotype frequency data obtained from short-read whole genome sequencing of about 61,000 Japanese individuals (Tadaka et al. [2])

  • 61KJPN-HLA: HLA allele frequency data obtained from short-read whole genome sequencing of about 61,000 Japanese individuals

  • 61KJPN-STR: Short Tandem Repeat allele frequency data obtained from short-read whole genome sequencing of about 61,000 Japanese individuals

  • JCNVv1: Copy number variation data obtained from short-read whole genome sequencing of 48,874 Japanese individuals

  • 8.3KJPN-SV: Allele and genotype frequency data of structural variations obtained from short-read whole genome sequencing of approximately 8,300 Japanese individuals

  • JSV1: Allele and genotype frequency data of structural variations obtained from 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

  • Correlation information among SNVs/INDELs calculated from 54KJPN and 8.3KJPN

  • 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 whole blood transcriptome: transcriptome analysis of approximately 500 Japanese whole blood samples (Aoki et al. [8])

  • ToMMo ISO-Seq: long-read transcriptome analysis of three Japanese male individuals (Otsuki et al. [9])

  • 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. [10], Saigusa et al. [11])

• Metabolome

  • Metabolome: 約 73,000人の日本人血漿サンプルのメタボローム解析データ (Koshiba et al. [10], Saigusa et al. [11], Saigusa et al. [12])

• Imaging

  • MRI: Volume information of each brain region based on MRI brain imaging for around 12,000 individuals

• 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. [13])

  • Metagenome 16S-v3/v4 (2022): Microbiome analysis of plaque and saliva samples (16S v3/v4 region analysis)

  • Metagenome 16S-v3/v4 (2023): Microbiome analysis of fecal samples samples (shotgun metagenome 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.