1.2. Datasets included in jMorp
At the time of writing, the following datasets are present in jMorp.
- Genome Variation
54KJPN: SNV/INDEL allele frequency and genotype frequency data obtained from short-read whole genome sequencing of about 54,000 Japanese individuals (Tadaka et al. [2])
54KJPN-HLA: HLA allele frequency data obtained from short-read whole genome sequencing of about 54,000 Japanese individuals
54KJPN-STR: Short Tandem Repeat allele frequency data obtained from short-read whole genome sequencing of about 54,000 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 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])
- Metabolome
Metabolome: Metabolome analysis results obtained from around 63,000 Japanese plasma samples (Koshiba et al. [9], Saigusa et al. [10], Saigusa et al. [11])
- 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. [12])
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.