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 mr1454 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
vg0410982826 sf0410973527 4 10982826 5.80E-17 NA
vg1001341384 sf1001340361 10 1341384 3.29E-16 NA
vg0408362316 sf0408357590 4 8362316 3.60E-16 NA
vg0141860740 sf0141859697 1 41860740 5.94E-16 NA
vg0231795631 sf0231789762 2 31795631 8.26E-16 NA
vg0407789423 sf0407784691 4 7789423 2.84E-12 NA
vg0717072590 sf0717071597 7 17072590 NA 3.40E-07
vg1116342312 sf1115877188 11 16342312 NA 1.75E-06
vg0410397733 sf0410388432 4 10397733 NA 2.16E-06
vg0729692653 sf0729691661 7 29692653 NA 3.92E-06