1.首先在SNP-Seek(https://snp-seek.irri.org/)中,进入Genotypes, 2.在Gen locus,输入基因ID(注意是LOC_类型的),并且可以在START和End中自行选择所要分析基因位置,然后在Show phenotype中选择是要分析的表型,完成后点击SEARCH. 3.分析好后,点击CSV,将结果下载下来。(切记在CSV文件中不要做任何处理,改文件格式...
SNP-Seek Resource for Rice ResearchLocedie Mansueto
2018). The physical positions of the 882 SNPs were used to extract a dataset of filtered SNPs for the entire 3 K-RG using the rice SNP-seek database (Mansueto et al. 2017). As a result, a total of 837 SNPs in common in both data sets were used for downstream analysis. The SNPs ...
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93...
SNP和等位基因信息被组织成一个SNP-Seek系统(http://www.oryzasnp.org/iric-portal/),该系统由Oracle数据库组成,该数据库具有SNP基因型接近600亿的行总数(20 M个SNP x 3 K水稻行)和Web界面,方便查询。该数据库允许快速检索给定基因组区域中所有变种的SNP等位基因,从预定的变种中查找不同的等位基因,并查询有...
Intact RNA-seq datasets were deposited in the NCBI Gene Expression Omnibus (GEO) under accession numberGSE168650. The Rice SNP-Seek Database is accessible athttps://snp-seek.irri.org/; the EnsemblPlants database is accessible athttp://plants.ensembl.org/index.html.Source dataare provided with...
The SNP data were downloaded from Rice SNP-Seek Database (https://snp-seek.irri.org/). The gene PAVs and structural variations were downloaded from the figshare database (doi: 10.6084/m9.figshare.c.3876022.v1). Characterizing variations To evaluate the population differentiation, FST per ...
et al. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res. 45, D1075–D1081 (2017). Article CAS Google Scholar Wang, W. S. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018). Article CAS Google ...
SNP-Seek database (Alexandrov et al.2014;www.oryzasnp.org/iric-portal). The SNP-Seek database provides a user-friendly resource to explore the genetic diversity of a large collection of germplasm accessions. Through this database, one can query by SNP haplotypes, germplasm accession names, ...
et al. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res. 45, D1075–D1081 (2016). Article PubMed PubMed Central CAS Google Scholar Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012)....