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 mr1919 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
vg0225928004 sf0225922135 2 25928004 1.47E-07 1.47E-07
vg0421078392 sf0420906445 4 21078392 1.27E-06 1.27E-06
vg0318766245 sf0318765005 3 18766245 2.65E-06 2.65E-06
vg0403328670 sf0403324273 4 3328670 2.68E-06 2.69E-06
vg1108752857 sf1108747467 11 8752857 4.03E-06 4.03E-06
vg0319690518 sf0319689029 3 19690518 4.96E-06 4.96E-06