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 mr1587 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
vg0505162615 sf0505162593 5 5162615 7.40E-08 7.40E-08
vg0313767191 sf0313765908 3 13767191 3.89E-07 3.89E-07
vg0618906581 sf0618905584 6 18906581 5.00E-07 5.00E-07
vg1201180694 sf1201179694 12 1180694 7.43E-07 7.43E-07
vg1210706721 sf1210704134 12 10706721 8.56E-07 8.56E-07
vg0133493808 sf0133492764 1 33493808 1.57E-06 1.57E-06
vg0518025487 sf0517964973 5 18025487 2.07E-06 2.08E-06