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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

JGAD000868

Type of data
Processed data of JGAD000495 (reference panel) by JGA (data for the TogoImputation reference panel)
Access criteria
Controlled-access (Type I)
Total data volume
6.2 GB
File formats
  • TAR
Research
hum0014
Date published
2024-08-28
Date modified
2024-08-28
DDBJ Search
JGAD000868 (opens in a new tab)
JGA Study
JGAS000381 (opens in a new tab)

Analysis method

WGS imputation panel (autosomes + X)

Materials and participants
WGS data (JGAD000495) of the biobank Japan project (N=1,964)
  • Subject count
    2990 (Individual)
  • Cohort
    BioBank Japan
Experimental method
WGS
Target
N/A
Reference genome
GRCh38
Mapping
bwa mem (version 0.7.15)
Read deduplication
GATK MarkDuplicates (version 4.1.0.0)
Realignment and base quality recalibration
N/A
Mapping quality
N/A
QC and filtering
Germline whole genome sequencing data were processed, and the aggregate VCF was calculated. Variants were then filtered based on the following conditions:
(1) Variants that did not pass the VQSR filter were excluded
(2) Multi-allelic sites were excluded
(3) Variants with a call rate below 95% were excluded
(4) Variants deviating from Hardy-Weinberg equilibrium (P < 1e-10) were excluded
(5) Variants with a minor allele count (MAC) less than 2 were excluded
Analysis method
GATK HaplotypeCaller -ERC GVCF (version 4.1.0.0)
The ploidy for variant call was set as follows:
Autosomes and pseudoautosomal regions (PARs): ploidy=2
Non-PARs on the X chromosome: ploidy=2 (female) and ploidy=1 (male)
Non-PARs on the Y chromosome: ploidy=1 (male)
Coverage (depth)
19.61x (± 5.41)
Variant count
21,596,248 variants
Autosomes: 21,157,732 variants
X chromosome: 438,516 variants
Processed data type
Reference panel
Variant calls
Dataset ID of original data
JGAD000220
JGAD000495
Processing method
List of processed data (Imputation reference)
Data use policy
NBDC data sharing policy (JGAP000001)