SNP-Seek database of SNPs derived from 3000 rice genomes.
Bottom Line: We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines firstname.lastname@example.org.Show MeSH
Related in: MedlinePlus
Mentions: Not all SNPs have been called in all varieties. Actually, the distribution of the called SNPs among varieties is bimodal, with one mode at about 18 M SNP calls corresponding to japonica varieties which are close to the reference genome, and the second peak at about 14 M corresponding to the other varieties (Figure 3).
Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines email@example.com.