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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.
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Dataset ID

NHA000176

Type of data
NGS (WGS)
Access criteria
Unrestricted-access
Total data volume
1.3 GB
File formats
  • TXT
  • ZIP
Research
hum0364
Date published
2022-08-29
Date modified
2022-08-29
Secondary ID
hum0364.v1.wgs-ms.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0364.v1.wgs-ms.v1.zip1.3 GB
hum0364.v1.wgs-ms.v1_Readme.txtREADME2.2 KB

Analysis method

WGS

Materials and participants
Publicly available WGS data of healthy individuals
SGDP: 276 samples
HGDP: 693 samples
Jomon people: 1 sample
  • Health status
    Healthy
  • Subject count
    970 (Individual)
  • Cohort
    HGDP, SGDP
  • Population
    Jomon
Sample description
Publicly available WGS data: SGDP, HGDP,Jomon
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
N/A
Fragmentation
N/A
Platform
N/A
Read type
N/A
Read length
N/A
Reference genome
GRCh37
Mapping
Bam files generated by SGDP and HGDP project were used in this study.
Read deduplication
Bam files generated by SGDP and HGDP project were used in this study.
Realignment and base quality recalibration
Performed by SGDP and HGDP. This study used the publicly available BAM files.
Mapping quality
Reads with a mapping quality of 20 or higher were used.
QC and filtering
MS covered by less than ten reads were considered insufficient depth, and we excluded samples if more than 4% had insufficient depth of MS.
Analysis method
MIVcall method
Coverage (depth)
HGDP and SGDP: 31.7x
Funadomari: 30.4x
Variant count
Autosomes: 733,900
Data use policy
NBDC data sharing policy (JGAP000001)