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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

JGAD000881

Type of data
Imputation reference panel for 3,256 Japanese WGS and 2,504 1000 Genome Project data
Access criteria
Controlled-access (Type I)
Total data volume
28.2 GB
File formats
  • VCF
Research
hum0014
Date published
2024-12-04
Date modified
2024-12-04
DDBJ Search
JGAD000881 (opens in a new tab)
JGA Study
JGAS000746 (opens in a new tab)

Analysis method

WGS + reference panel (autosomes + X)

Materials and participants
[WGS]
Subjects registered in BioBank Japan: 3,256 individuals
including followed data
- 1,026 individuals (JGAD000220)
- 256 gastric cancer patients registered in BBJ 1st cohort (JGAD000831)
- 1,765 myocardial infarction patients and 199 dementia patients (JGAD000495)
[reference panel]
- WGS data of the BBJ 1st cohort (N=3,256)
- WGS data of 1KGP p3v5 ALL (N=2,504) (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/)
  • Health status
    Mixed
  • Subject count
    3256 (Individual)
  • Cohort
    1000 Genomes Project, 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 2500
Illumina HiSeq X
Read type
Paired-end
Read length
125 bp
126 bp
151 bp
161 bp
Reference genome
GRCh37
Mapping
BWA mem 0.7.12
Read deduplication
Picard 2.10.6
Realignment and base quality recalibration
GATK v.3.2-2
Mapping quality
Reads with MAPQ<20 were excluded at variant calling with GATK 3.7 HaplotypeCaller
QC and filtering
We set exclusion criteria for genotypes sequenced as follows:
(1) DP < 5, (2) GQ < 20, or (3) DP > 60 and GQ < 95, and regarded these genotypes as missing.
Variants with call rates < 90% were excluded before variant quality score recalibration (VQSR).
After VQSR, variants located in low-complexity regions (LCR), as defined by mdust software, were excluded.
Finally, we used BEAGLE to impute missing genotypes.
Analysis method
GATK 3.7 HaplotypeCaller
Coverage (depth)
30x
15x
Variant count
4,057,373 (variants autosomes)
44,444 (variants X chromosome)
66,863,693 (variants autosomes)
3,206,807 (variants X chromosome)
74,210,602 variants
Autosomes: 70,958,158 variants
X chromosome: 3,252,444 variants
Processed data type
Reference panel
Data use policy
NBDC data sharing policy (JGAP000001)