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RiceVarMap: a comprehensive database of rice genomic variations
Open accessAbstract
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast model-based estimation of ancestry in unrelated individuals
Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898
Cited by
Kuang, Y., Li, S., Ren, B., Yan, F., Spetz, C., Li, X., Zhou, X., & Zhou, H. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.01.010 · Cited by 266
Metadata
- Authors
- Zhao, H., Yao, W., Ouyang, Y., Yang, W., Wang, G., Lian, X., Xing, Y., Chen, L., & Xie, W.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-01
- Volume
- 43
- Issue
- D1
- Pages
- D1018-D1022
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2130774313
- Cited by
- 350
- References
- 2
- FWCI
- 7.53
- Type
- journal article
- Language
- en
- Open access
- gold
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- Zhao, H., Yao, W., Ouyang, Y., Yang, W., Wang, G., Lian, X., Xing, Y., Chen, L., & Xie, W. (2015). RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Research. https://doi.org/10.1093/nar/gku894
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