SoyMine: Home

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Search this mine. Enter names, identifiers or keywords. Examples: Glyma.01G086900, Glyma.01G086900.1, BARCSOYSSR_04_1400, Seed yield 15-5, R-GMA-8879007.1, David Grant.

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Welcome to the LIS SoyMine!

This mine integrates many types of data for soybean. It is currently under development by LIS, built from the LIS chado database (genomic data) and the SoyBase database (genetic data) as well as some flat files. Contact Sam Hokin shokin at ncgr dot org.

Click here to see the US Germplasm genotyping study, added in v0.10. Let us know how you'd like us to improve the genotype matrix viewer!

Latest updates (v0.10, October 2018)

We've added the big BARC_1059007 genotyping study, which genotyped all of the GRIN soybean accessions using the SoySNP50K BeadChip.
To support the above, we've imported the GRIN soybean lines (as GenotypingLine) along with their Phenotype information.
New displayer: a genotyping matrix viewer for the genotyping study
New displayer: an allele counter on genetic marker report pages
New displayer: a scatterplot of QTL p-values on GWAS experiments (think Manhattan plot)

A note about "Organism"
InterMine associates an "Organism" with a distinct genome. Therefore, you will find many soybean "organisms" in this mine, which represent different varieties. However, some quantities, like genetic markers, are not associated with a specific variety; in that case, they are associated with and placed on the reference Williams82 genome.