{"id":"NHA000176","research":"hum0364","url":"https://humandbs.dbcls.jp/dataset/NHA000176","datePublished":"2022-08-29","dateModified":"2022-08-29","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"unrestricted-access","label":{"ja":"非制限公開","en":"Unrestricted-access"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"NGS（WGS）","en":"NGS (WGS)"}}],"experiments":[{"label":"WGS","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"非制限公開されているヒトのWGS解析データ（健常者）\nSGDP：276名\nHGDP：693名\n縄文人：1名","en":"Publicly available WGS data of healthy individuals\nSGDP: 276 samples\nHGDP: 693 samples\nJomon people: 1 sample"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":970,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"individual","label":{"ja":"人数","en":"Individual"}}]},{"key":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"sgdp","label":{"en":"SGDP"}},{"code":"hgdp","label":{"en":"HGDP"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"jomon","label":{"ja":"縄文人","en":"Jomon"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"非制限公開されているSGDP、HGDP、縄文人のWGS解析データ（NGS）","en":"Publicly available WGS data: SGDP, HGDP,Jomon"}},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"normal","label":{"ja":"非腫瘍","en":"Normal"}}]},{"key":"sample-provider","label":{"ja":"試料の入手元","en":"Sample provider"},"type":"text","text":{"ja":null,"en":null}},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"wgs","label":{"en":"WGS"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":null,"en":null}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":null},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":null,"en":null}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":null},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":null},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":null},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"SGDPやHGDPにより行われた。本研究では公開されているbamファイルを用いた。","en":"Bam files generated by SGDP and HGDP project were used in this study."}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"SGDPやHGDPにより行われた。本研究では公開されているbamファイルを用いた。","en":"Bam files generated by SGDP and HGDP project were used in this study."}},{"key":"calibration-for-re-alignment-and-base-quality","label":{"ja":"再アライメント・塩基品質補正","en":"Realignment and base quality recalibration"},"type":"text","text":{"ja":"SGDPやHGDPにより行われた。本研究では公開されているbamファイルを用いた。","en":"Performed by SGDP and HGDP. This study used the publicly available BAM files."}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"20以上のリードを用いた。","en":"Reads with a mapping quality of 20 or higher were used."}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"10本未満のリードで覆われているMSは深度不足とした。全MSのうち深度不足が4%以上のサンプルは解析から除いた。","en":"MS covered by less than ten reads were considered insufficient depth, and we excluded samples if more than 4% had insufficient depth of MS."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"MIVcall法","en":"MIVcall method"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":31.7,"unit":"x","high":null,"prefix":{"ja":"HGDPおよびSGDP: ","en":"HGDP and SGDP: "}},{"value":30.4,"unit":"x","high":null,"prefix":{"ja":"Funadomari: ","en":"Funadomari: "}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":733900,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}}]},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"zip","label":{"en":"ZIP"}}]}