{"id":"JGAD000362","research":"hum0248","url":"https://humandbs.dbcls.jp/dataset/JGAD000362","datePublished":"2020-11-04","dateModified":"2020-11-18","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-2","label":{"ja":"制限公開（Type II）","en":"Controlled-access (Type II)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"日本人基準ゲノム配列","en":"Japanese reference genome sequence"}}],"experiments":[{"label":"WGS","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"日本人健常男性：3名","en":"3 Japanese male individuals"}},{"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 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(Covaris)"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"bionano-irys","label":{"en":"Bionano Irys"}},{"code":"bionano-saphyr","label":{"en":"Bionano Saphyr"}},{"code":"illumina-hiseq-2500","label":{"en":"Illumina HiSeq 2500"}},{"code":"pacbio-rs-ii","label":{"en":"PacBio RS II"}}]},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":[{"code":"paired-end","label":{"ja":"ペアエンド","en":"Paired-end"}}]},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":[{"value":10000,"unit":"bp","high":null,"prefix":{"ja":"PacBio: ","en":"PacBio: "}},{"value":10589,"unit":"bp","high":null,"prefix":{"ja":"- jg1a: ","en":"- jg1a: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":10066,"unit":"bp","high":null,"prefix":{"ja":"- jg1b: ","en":"- jg1b: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":9226,"unit":"bp","high":null,"prefix":{"ja":"- jg1c: ","en":"- jg1c: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":146000,"unit":"bp","high":null,"prefix":{"ja":"Bionano: ","en":"Bionano: "},"suffix":{"ja":" (超)","en":" (More than)"}},{"value":318216,"unit":"bp","high":null,"prefix":{"ja":"- jg1a.BspQI: ","en":"- jg1a.BspQI: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":228101,"unit":"bp","high":null,"prefix":{"ja":"- jg1a.BssSI: ","en":"- jg1a.BssSI: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":169138,"unit":"bp","high":null,"prefix":{"ja":"- jg1b.DLS: ","en":"- jg1b.DLS: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":146026,"unit":"bp","high":null,"prefix":{"ja":"- jg1c.DLS: ","en":"- jg1c.DLS: "},"suffix":{"ja":" (平均)","en":" (mean)"}},{"value":162,"unit":"bp","high":null,"prefix":{"ja":"Illumina: ","en":"Illumina: "}},{"value":259,"unit":"bp","high":null,"prefix":{"ja":"Illumina: ","en":"Illumina: "}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"PacBio：Falconソフトウェア内でのQC（length_cutoff = 9000, length_cutoff_pr = 15000）\nBionano：BionanoSolveソフトウェア内でのQC (default config)\nIllumina：特になし","en":"PacBio: QC with Falcon software with length_cutoff = 9000, length_cutoff_pr = 15000\nBionano: QC with BionanoSolve software with default settings\nIllumina: NA"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"hs37d5とJG1の常染色体およびX染色体における比較；minimap2, paftools\n① デノボアセンブリ(リードによる全ゲノム塩基配列の決定)\n①-1 長鎖リード解読技術によるコンティグ作成: Pacific Bioscience社の一分子リアルタイムシークエンシング技術(SMRTシークエンシング技術)と、Falconソフトウェアによるデノボアセンブリ。\n①-2 解読したゲノム配列間の結合: Bionano Genomics社のオプティカルマッピング技術とBionanoSolveソフトウェアによるデノボアセンブリ\n② ①-1と①-2を用いてハイブリッドスキャフォールドの作成(BionanoSolveソフトウェアによる)\n③ エラー除去: IlluminaのPair-end配列情報を用いたエラー修正(Pilonソフトウェア)\n④ 位置・配向情報の取得: Illuminaリードによるメイトペアライブラリー技術(Bowtie2ソフトウェア)\n⑤ ②に③と④の情報を加えることで、1名ずつのドラフト配列の決定、ならびに、3者間で解読できなかった領域の補完(Metassembler)\n⑥ 配列スキャフォールドと染色体との対応付け(アンカリング): 観測された組み換えの頻度から遺伝子やマーカーの並び順と距離を示す遺伝地図(連鎖地図)、放射線ハイブリッド地図、(gPCRソフトウェアによる)","en":"SNVs between hs37d5 and JG1 in the autosomes and X chromosome were called using minimap2 and paftools software\n1. highly contiguous de novo assembly:\n1) PacBio long reads were de novo assembled to yield primary contigs\n2) Bionano raw data were also de novo assembled (independent of the PacBio assembly) to yield genome maps\n3) the PacBio-derived contigs were scaffolded by the Bionano genome maps\n2. Polishing the hybrid scaffolds with Illumina short reads (paired-end)\n3. Integrating and filling the gaps of the hybrid scaffolds of each individual with an aid of mate pair Illumina short reads\n4. meta-assembly with Metassembler software\n5. Anchoring scaffolds to chromosomes with genetic and radiation hybrid maps"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":122,"unit":"x","high":null,"prefix":{"ja":"PacBio: ","en":"PacBio: "},"suffix":{"ja":" (超)","en":" (More than)"}},{"value":122,"unit":"x","high":null,"prefix":{"ja":"- jg1a: ","en":"- jg1a: "}},{"value":123,"unit":"x","high":null,"prefix":{"ja":"- jg1b: ","en":"- jg1b: "}},{"value":128,"unit":"x","high":null,"prefix":{"ja":"- jg1c: ","en":"- jg1c: "}},{"value":123,"unit":"x","high":null,"prefix":{"ja":"Bionano: ","en":"Bionano: "},"suffix":{"ja":" (超)","en":" (More than)"}},{"value":123,"unit":"x","high":null,"prefix":{"ja":"- jg1a.BspQI: ","en":"- jg1a.BspQI: "}},{"value":140,"unit":"x","high":null,"prefix":{"ja":"- jg1a.BssSI: ","en":"- jg1a.BssSI: "}},{"value":160,"unit":"x","high":null,"prefix":{"ja":"- jg1b: ","en":"- jg1b: "}},{"value":175,"unit":"x","high":null,"prefix":{"ja":"- jg1c: ","en":"- jg1c: "}},{"value":26,"unit":"x","high":null,"prefix":{"ja":"Illumina ペアエンド: ","en":"Illumina paired end: "},"suffix":{"ja":" (超)","en":" (More than)"}},{"value":29,"unit":"x","high":null,"prefix":{"ja":"- jg1a.162PE: ","en":"- jg1a.162PE: "}},{"value":26,"unit":"x","high":null,"prefix":{"ja":"- jg1a.259PE: ","en":"- jg1a.259PE: "}},{"value":31,"unit":"x","high":null,"prefix":{"ja":"- jg1b.162PE: ","en":"- jg1b.162PE: "}},{"value":28,"unit":"x","high":null,"prefix":{"ja":"- jg1b.259PE: ","en":"- jg1b.259PE: "}},{"value":31,"unit":"x","high":null,"prefix":{"ja":"- jg1c.162PE: ","en":"- jg1c.162PE: "}},{"value":26,"unit":"x","high":null,"prefix":{"ja":"- jg1c.259PE: ","en":"- jg1c.259PE: "}},{"value":12,"unit":"x","high":null,"prefix":{"ja":"Illumina メイトペア: ","en":"Illumina mate-pair: "},"suffix":{"ja":" (超)","en":" (More than)"}},{"value":13,"unit":"x","high":null,"prefix":{"ja":"- jg1a: ","en":"- jg1a: "}},{"value":12,"unit":"x","high":null,"prefix":{"ja":"- jg1b: ","en":"- jg1b: "}},{"value":12,"unit":"x","high":null,"prefix":{"ja":"- jg1c: ","en":"- jg1c: "}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":8697,"unit":null,"high":null,"prefix":{"ja":"50 bp 超の挿入: ","en":"Insertions longer than 50 bp: "}},{"value":6190,"unit":null,"high":null,"prefix":{"ja":"50 bp 超の欠失: ","en":"Deletions longer than 50 bp: "}},{"value":2501575,"unit":null,"high":null,"suffix":{"ja":" SNVs","en":" SNVs"}}]},{"key":"insdc-sequence-accession","label":{"ja":"INSDC配列 Accession","en":"INSDC Sequence Accession"},"type":"text","text":{"ja":"AP023461-AP024084","en":"AP023461-AP024084"}},{"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)"}},{"code":"jgap000011-policy","label":{"ja":"JGAP000011 Policy","en":"JGAP000011 Policy"}}]}]}],"dataVolume":9,"fileFormats":[{"code":"txt","label":{"en":"TXT"}}]}