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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

JGAD000410

Type of data
bam/gvcf data of WGS (JGAD000220)
Access criteria
Controlled-access (Type I)
Total data volume
53.3 TB
File formats
  • BAM
  • BAI
  • VCF
  • TBI
Research
hum0014
Date published
2021-06-21
Date modified
2021-08-25
DDBJ Search
JGAD000410 (opens in a new tab)
JGA Study
JGAS000114 (opens in a new tab)

Analysis method

WGS

Materials and participants
1,026 individuals
  • Health status
    Affected
  • Subject count
    1026 (Individual)
  • Cohort
    BioBank Japan
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
160 bp
Reference genome
GRCh37
Mapping
BWA mem 0.7.12
Read deduplication
Picard 2.10.6
Realignment and base quality recalibration
GATK 3.7
Mapping quality
Reads with MAPQ<20 were excluded at variant calling with GATK 3.7 HaplotypeCaller
QC and filtering
Data with bad base quality and high %GC content were removed.
Alignment:
Data matched for the following conditions were removed.
- Low mapping rate
- Different insert size
- Gender information mismatch between meta-data and genotype data
- Suspected sex chromosome aberration
Genotyping:
GATK's best practices include a variant filtering step following Variant Quality Score Recalibration (VQSR)
- DP/GP (DP < 5, GQ < 20, DP > 60, GQ < 95)
- Heterozygosity (F>=0.05)
- Hardy-Weinberg equilibrium (p < 10^-6)
- Repeat & Low Complexity
Principal Component Analysis (PCA):
PCA was performed with individuals included in the 1000 genomes project and outliers from Japanese cluster were removed.

After these filtering steps, variants located in the regions listed as the HighConfidenceRegion (Genome-In-A-Bottle project) were flagged.
Analysis method
GATK 3.7 HaplotypeCaller
Coverage (depth)
31.8x
Variant count
Autosomes: 10,202,908
X chromosome: 410,435
Autosomes: 76,768,387
X chromosome: 2,898,518
Processed data type
Alignment
Variant calls
Data summary
Whole genome sequencing analyzed data included in the JGAD000220 were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. This project is an initiative of the GEnome Medical Alliance Japan (GEM Japan, GEM-J). Learn more
Dataset ID of processed data
JGAD000690
JGAD000758 (joint call)
Processing method
List of processed data (Whole Genome Sequencing Analysis)
Data use policy
NBDC data sharing policy (JGAP000001)