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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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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

NHA000067

Type of data
(1) Allele frequencies from WGS
Access criteria
Unrestricted-access
Total data volume
318 MB
File formats
  • XLSX
  • ZIP
Research
hum0056
Date published
2018-03-30
Date modified
2018-03-30
Secondary ID
hum0056.v1.freq.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0056.v1.freq.v1.zip318 MB
hum0056_header.xlsxDictionary file13.3 KB

Analysis method

WGS

Materials and participants
IMM cohort: 197 individuals
  • Health status
    Healthy
  • Subject count
    197 (Individual)
Sample description
DNAs extracted from 102 monocytes, 102 CD4+ T cells, and 94 neutrophils
  • Tissue
    CD4+ T cell, Monocyte, Neutrophil
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
Ultrasonic fragmentation (Covaris LE220)
Platform
Illumina HiSeq 2500
Illumina HiSeq X
Read type
Paired-end
Read length
162 bp
72 neutrophil samples: 150 bp
Reference genome
GRCh37
Mapping
Bowtie2 (version 2.1.0)
Read deduplication
none
Realignment and base quality recalibration
none
QC and filtering
qMiSeq*1
Analysis method
Bcftools software (ver. 0.1.17-dev)
Read count
230,956,735,490 / 228,318,012,630
(Monocytes: 58,859,522,366 / 57,737,359,722)
(CD4+ T cells: 58,964,563,094 / 57,845,976,317)
(neutrophils: 113,132,650,030 / 112,734,676,591)
*mapped reads: a read which had multiple mapped locations was aligned to one site randomly.
Coverage (depth)
40.9x
Variant count
Monocytes: 8,129,415 SNPs
CD4-positive T lymphocytes: 8,137,443 SNPs
Neutrophils: 8,175,808 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)