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 mr1444 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
vg0807421509 sf0807420514 8 7421509 1.08E-07 4.30E-07
vg0417775732 sf0417603769 4 17775732 3.23E-07 1.75E-06
vg0127831218 sf0127830174 1 27831218 5.82E-07 4.27E-06
vg0907725133 sf0907724133 9 7725133 9.63E-07 3.50E-06
vg0523575244 sf0523512665 5 23575244 NA 1.07E-06