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Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1459 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0327935681 sf0327928735 3 27935681 3.19E-07 3.19E-07
vg0327981236 sf0327974290 3 27981236 1.02E-06 1.02E-06
vg0130302150 sf0130301105 1 30302150 1.37E-06 1.37E-06
vg0322468437 sf0322466926 3 22468437 1.79E-06 1.79E-06
vg0217798267 sf0217792398 2 17798267 3.81E-06 3.81E-06
vg0622395868 sf0622394871 6 22395868 4.20E-06 4.21E-06