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 mr1838 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
vg0205295837 sf0205295835 2 5295837 1.17E-12 4.57E-08
vg0128988129 sf0128987084 1 28988129 2.56E-08 NA
vg0414792045 sf0414782759 4 14792045 3.60E-08 1.77E-06
vg0813412700 sf0813410253 8 13412700 9.13E-07 3.33E-06
vg1119943497 sf1119477420 11 19943497 2.25E-06 4.73E-06