AMAP : A pipeline for whole-genome mutation detection in Arabidopsis thaliana
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- Ishii Kotaro
- RIKEN Nishina Center
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- Kazama Yusuke
- RIKEN Nishina Center
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- Hirano Tomonari
- RIKEN Nishina Center Faculty of Agriculture, University of Miyazaki
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- Hamada Michiaki
- Faculty of Science and Engineering, Waseda University
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- Ono Yukiteru
- IMSBIO Co., Ltd.
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- Yamada Mieko
- RIKEN Nishina Center
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- Abe Tomoko
- RIKEN Nishina Center
書誌事項
- タイトル別名
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- AMAP: A pipeline for whole-genome mutation detection in <i>Arabidopsis thaliana</i>
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<p>Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consuming process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator). Thus, all types of mutations such as base substitution, deletion, insertion, translocation and chromosomal rearrangement can be detected by AMAP. In addition, AMAP automatically distinguishes false positives by comparing lists of candidate mutations in sequenced mutants. We tested AMAP by inputting already analyzed read data derived from three individual Arabidopsis thaliana mutants and confirmed that all true mutations were included in the list of candidate mutations. The result showed that the number of false positives was reduced to 12% of that obtained in a previous analysis that lacked a process of reducing false positives. Thus, AMAP will accelerate not only the analysis of mutation induction by individual mutagens but also the process of forward genetics.</p>
収録刊行物
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- Genes & Genetic Systems
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Genes & Genetic Systems 91 (4), 229-233, 2016
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詳細情報 詳細情報について
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- CRID
- 1390282680450244608
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- NII論文ID
- 130005450121
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- NII書誌ID
- AA11077421
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- ISSN
- 18805779
- 13417568
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- NDL書誌ID
- 028000634
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- PubMed
- 27452041
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- NDL
- Crossref
- PubMed
- CiNii Articles
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- 抄録ライセンスフラグ
- 使用不可