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SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

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SNP distribution by varieties. The major peak shows that about 14 M SNPs have been called in most varieties. The bimodal plot indicates that a fraction of SNPs are missing in some varieties, likely due to lack of mapped reads in variable regions.
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Figure 3: SNP distribution by varieties. The major peak shows that about 14 M SNPs have been called in most varieties. The bimodal plot indicates that a fraction of SNPs are missing in some varieties, likely due to lack of mapped reads in variable regions.

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).


SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

SNP distribution by varieties. The major peak shows that about 14 M SNPs have been called in most varieties. The bimodal plot indicates that a fraction of SNPs are missing in some varieties, likely due to lack of mapped reads in variable regions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383887&req=5

Figure 3: SNP distribution by varieties. The major peak shows that about 14 M SNPs have been called in most varieties. The bimodal plot indicates that a fraction of SNPs are missing in some varieties, likely due to lack of mapped reads in variable regions.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

Show MeSH
Related in: MedlinePlus