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 mr1725 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
vg1016323758 sf1016252534 10 16323758 1.87E-08 NA
vg0200808087 sf0200808087 2 808087 5.08E-08 6.88E-06
vg0200814842 sf0200814842 2 814842 5.77E-08 3.84E-06
vg1216993343 sf1216987297 12 16993343 5.89E-08 NA
vg1004612953 sf1004629491 10 4612953 1.49E-06 NA