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 mr1789 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
vg0207745017 sf0207745016 2 7745017 1.73E-35 2.04E-08
vg1224911869 sf1224878323 12 24911869 7.95E-35 NA
vg0129744626 sf0129743581 1 29744626 2.64E-34 NA
vg0311491162 sf0311489880 3 11491162 1.24E-33 NA
vg0125866751 sf0125865707 1 25866751 1.42E-33 NA
vg0228204274 sf0228198405 2 28204274 NA 7.89E-07
vg1109631523 sf1109626100 11 9631523 NA 9.72E-07
vg0707996084 sf0707995089 7 7996084 NA 1.96E-06
vg0316269128 sf0316267775 3 16269128 NA 2.60E-06
vg0316321682 sf0316320329 3 16321682 NA 5.56E-06