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 mr1764 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
vg0805946030 sf0805945033 8 5946030 1.75E-09 2.72E-07
vg0805900956 sf0805899959 8 5900956 1.77E-08 7.13E-08
vg0207698155 sf0207698154 2 7698155 3.19E-08 9.19E-06
vg1001247868 sf1001246845 10 1247868 2.21E-07 2.05E-06
vg0324965295 sf0324963375 3 24965295 4.03E-07 3.00E-06
vg0509233251 sf0509233180 5 9233251 2.53E-06 1.96E-06