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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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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

JGAD000362

Type of data
Japanese reference genome sequence
Access criteria
Controlled-access (Type II)
Total data volume
9 B
File formats
  • TXT
Research
hum0248
Date published
2020-11-04
Date modified
2020-11-18
DDBJ Search
JGAD000362 (opens in a new tab)
JGA Study
JGAS000259 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Accession-Numbers.txt14.8 KB

Analysis method

WGS

Materials and participants
3 Japanese male individuals
  • Health status
    Healthy
  • Subject count
    3 (Individual)
  • Population
    Japanese
  • Sex
    Male
Sample description
gDNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
DNA Template Prep Kit 2.0
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
Illumina: Ultrasonic fragmentation (Covaris)
Platform
Bionano Irys
Bionano Saphyr
Illumina HiSeq 2500
PacBio RS II
Read type
Paired-end
Read length
PacBio: 10 kbp
- jg1a: 10,589 bp (mean)
- jg1b: 10,066 bp (mean)
- jg1c: 9226 bp (mean)
Bionano: 146 kbp (More than)
- jg1a.BspQI: 318,216 bp (mean)
- jg1a.BssSI: 228,101 bp (mean)
- jg1b.DLS: 169,138 bp (mean)
- jg1c.DLS: 146,026 bp (mean)
Illumina: 162 bp
Illumina: 259 bp
Reference genome
GRCh37
QC and filtering
PacBio: QC with Falcon software with length_cutoff = 9000, length_cutoff_pr = 15000
Bionano: QC with BionanoSolve software with default settings
Illumina: NA
Analysis method
SNVs between hs37d5 and JG1 in the autosomes and X chromosome were called using minimap2 and paftools software
1. highly contiguous de novo assembly:
1) PacBio long reads were de novo assembled to yield primary contigs
2) Bionano raw data were also de novo assembled (independent of the PacBio assembly) to yield genome maps
3) the PacBio-derived contigs were scaffolded by the Bionano genome maps
2. Polishing the hybrid scaffolds with Illumina short reads (paired-end)
3. Integrating and filling the gaps of the hybrid scaffolds of each individual with an aid of mate pair Illumina short reads
4. meta-assembly with Metassembler software
5. Anchoring scaffolds to chromosomes with genetic and radiation hybrid maps
Coverage (depth)
PacBio: 122x (More than)
- jg1a: 122x
- jg1b: 123x
- jg1c: 128x
Bionano: 123x (More than)
- jg1a.BspQI: 123x
- jg1a.BssSI: 140x
- jg1b: 160x
- jg1c: 175x
Illumina paired end: 26x (More than)
- jg1a.162PE: 29x
- jg1a.259PE: 26x
- jg1b.162PE: 31x
- jg1b.259PE: 28x
- jg1c.162PE: 31x
- jg1c.259PE: 26x
Illumina mate-pair: 12x (More than)
- jg1a: 13x
- jg1b: 12x
- jg1c: 12x
Variant count
Insertions longer than 50 bp: 8697
Deletions longer than 50 bp: 6190
2,501,575 SNVs
INSDC Sequence Accession
AP023461-AP024084
Data use policy
JGAP000011 Policy
NBDC data sharing policy (JGAP000001)