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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000077

Type of data
Allele frequencies of SNVs/Indels on autosomal chromosomes, X-chromosome, and mitochondrial DNA in 3552 participants
Access criteria
Unrestricted-access
Total data volume
2.5 GB
File formats
  • ZIP
Research
hum0015
Date published
2019-01-11
Date modified
2019-01-11
Secondary ID
hum0015.v3.3.5kjpnv2.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
metadata.zipmetadata3.5 KB
tommo-3.5kjpnv2-20181105-af_indelall-autosome.zipAllele frequencies of Indels (autosomes)468 MB
tommo-3.5kjpnv2-20181105-af_indelall-chrX_PAR2.zipAllele frequencies of Indels (X-chromosome [PAR1+PAR2])19.7 MB
tommo-3.5kjpnv2-20181105-af_indelall-chrX_PAR3.zipAllele frequencies of Indels (X-chromosome [PAR1+XTR+PAR2])18.7 MB
tommo-3.5kjpnv2-20181105-af_snvall-autosome.zipAllele frequencies of SNVs (autosomes)1.8 GB
tommo-3.5kjpnv2-20181105-af_snvall-chrMT.zipAllele frequencies of SNVs (mitochondrial DNA)58.1 KB
tommo-3.5kjpnv2-20181105-af_snvall-chrX_PAR2.zipAllele frequencies of SNVs (X-chromosome [PAR1+PAR2])70.2 MB
tommo-3.5kjpnv2-20181105-af_snvall-chrX_PAR3.zipAllele frequencies of SNVs (X-chromosome [PAR1+XTR+PAR2])71.9 MB

Analysis method

WGS

Materials and participants
3552 individuals from the general populations in Japan
  • Health status
    Healthy
  • Subject count
    3552 (Individual)
  • Population
    Japanese
Sample description
gDNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
Ultrasonic fragmentation (Covaris LE220)
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
162 bp
259 bp
Reference genome
GRCh37
Mapping
N/A
Mapping quality
N/A
QC and filtering
quantitative MiSeq (doi: 10.1016/j.ab.2014.08.015)
Analysis method
N/A
Coverage (depth)
27.2x (162PE)
21.3x (259PE)
Variant count
Autosomes: 50,500,000 SNVs + Indels (Approx.)
X chromosome: 2,000,000 SNVs + Indels (Approx.)
Mitochondria: 2500 SNVs (Approx.)
Data use policy
NBDC data sharing policy (JGAP000001)