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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

JGAD000777

Type of data
WGS for 1,007 individuals
Access criteria
Controlled-access (Type I)
Total data volume
41.6 TB
File formats
  • FASTQ
  • VCF
Research
hum0014
Date published
2023-11-09
Date modified
2023-11-09
DDBJ Search
JGAD000777 (opens in a new tab)
JGA Study
JGAS000647 (opens in a new tab)

Analysis method

WGS

Materials and participants
1,007 individuals from BBJ 1st cohort
  • Health status
    Affected
  • Subject count
    1007 (Individual)
  • Cohort
    BioBank Japan
  • Population
    Japanese
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
BWA-MEM (version 0.7.13)
Read deduplication
Picard 2.10.10
Realignment and base quality recalibration
GATK 3.8
Mapping quality
Reads with MAPQ<20 were excluded at variant calling with GATK 3.8 HaplotypeCaller
QC and filtering
- Autosomal Chromosomes, X PAR, X NonPAR female
- Set missing genotypes with DP < 2 or GQ < 20
- call rate < 90% were excluded
- X NonPAR male, Y
- Set missing genotypes with DP < 1 or GQ < 20
- call rate < 90% were excluded
- X NomPAR
HWE_P of female
Analysis method
GATK Haplotype Caller (version 3.8)
Coverage (depth)
19.93455x
Variant count
Autosomes: 71,643,487 (Record numbers including AC=0)
X PAR: 82,997 (Record numbers including AC=0)
X nonPAR: 2,618,495 (Record numbers including AC=0)
Y chromosome: 171,271 (Record numbers including AC=0)
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)