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 mr1666 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
vg0430989073 sf0430803953 4 30989073 1.82E-19 2.91E-06
vg0430942143 sf0430757023 4 30942143 3.31E-19 1.68E-06
vg0104592595 sf0104591595 1 4592595 1.65E-16 1.22E-06
vg0608189642 sf0608188643 6 8189642 5.85E-16 NA
vg0501165891 sf0501165875 5 1165891 9.28E-16 NA
vg0321323667 sf0321322177 3 21323667 1.23E-15 NA
vg0502049752 sf0502049734 5 2049752 4.93E-14 1.13E-06
vg0826359362 sf0826356648 8 26359362 NA 2.29E-06
vg0407913349 sf0407908618 4 7913349 NA 8.02E-06