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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

JGAD000679

Type of data
Processed data of JGAD000220 (reference panel) by JGA (data for the TogoImputation reference panel)
Access criteria
Controlled-access (Type I)
Total data volume
33.3 GB
File formats
  • TAR
Research
hum0014
Date published
2023-01-26
Date modified
2023-01-26
DDBJ Search
JGAD000679 (opens in a new tab)
JGA Study
JGAS000114 (opens in a new tab)

Analysis method

WGS reference panel (autosomes + X)

Materials and participants
  • Subject count
    1037 (Individual)
  • Cohort
    1000 Genomes Project, BioBank Japan
Experimental method
WGS
Target
N/A
Reference genome
GRCh37
Mapping
BWA-MEM (version 0.7.5a)
Read deduplication
picard (versions 1.106)
Realignment and base quality recalibration
GATK (ver.3.2-2)
Mapping quality
MAPQ < 20 were excluded (HaplotypeCaller)
QC and filtering
We set exclusion criteria for genotypes 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, we excluded 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 HaplotypeCaller (version 3.2-2)
Coverage (depth)
30x (aimed at depth)
Variant count
61,608,817 variants
Autosomes: 59,387,070 variants
X chromosome: 2,221,747 variants
Processed data type
Reference panel
Variant calls
Dataset ID of original data
JGAD000220
Processing method
List of processed data (Imputation reference)
Data use policy
NBDC data sharing policy (JGAP000001)