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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

JGAD000873

Type of data
Imputation reference panel for 7,472 Japanese WGS and 2,504 1000 Genome Project data
Access criteria
Controlled-access (Type I)
Total data volume
40.5 GB
File formats
  • VCF
Research
hum0014
Date published
2024-11-29
Date modified
2024-11-29
DDBJ Search
JGAD000873 (opens in a new tab)
JGA Study
JGAS000738 (opens in a new tab)

Analysis method

WGS + reference panel (autosomes)

Materials and participants
[WGS]
Subjects registered in BioBank Japan: 7,472 individuals
15-30x depth: 3,256 individuals, 3x depth: 4,216 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)
- 2,157 diabetes patients registered in BBJ 1st cohort (JGAD000833)
- 2,059 gastric cancer patients registered in BBJ 1st cohort (JGAD000834)
[reference panel]
- WGS data of the BBJ 1st cohort (N=7,472)
- WGS data of 1KGP p3v5 ALL (N=2,504) (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/)
  • Health status
    Affected
  • Subject count
    7472 (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
15-30x depth: BWA mem 0.7.12
3x depth: BWA mem 0.7.5a
Read deduplication
15-30x depth: Picard 2.10.6
3x depth: Picard 1.106, 2.5.0
Realignment and base quality recalibration
GATK v.3.2-2
Mapping quality
15-30x depth: Reads with MAPQ<20 were excluded at variant calling with GATK 3.7 HaplotypeCaller
3x depth: Reads with MAPQ<20 were excluded at variant calling with GotCloud
QC and filtering
We set exclusion criteria for genotypes sequenced at high depth (30x and 15x) 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 in the high depth (30x) dataset.
Finally, we used BEAGLE to impute missing genotypes.
Analysis method
15-30x depth: GATK 3.7 HaplotypeCaller
3x depth: GotCloud v1.17.5
Coverage (depth)
30x
15x
3x
Variant count
4,535,276
80,753,886
85,328,475 variants
Data use policy
NBDC data sharing policy (JGAP000001)