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 mr1556 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 4.53E-09 6.99E-07
vg0805900956 sf0805899959 8 5900956 8.25E-09 2.88E-08
vg0207698155 sf0207698154 2 7698155 5.07E-08 NA
vg0716717405 sf0716716412 7 16717405 7.52E-08 NA
vg0324965295 sf0324963375 3 24965295 2.73E-07 2.20E-06
vg1001247868 sf1001246845 10 1247868 3.29E-07 3.27E-06
vg0904643511 sf0904642511 9 4643511 1.52E-06 4.76E-06
vg0509233251 sf0509233180 5 9233251 2.95E-06 2.50E-06