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 mr1325 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
vg0315486151 sf0315484798 3 15486151 1.90E-16 8.74E-07
vg0323474238 sf0323472412 3 23474238 3.35E-16 NA
vg0124307645 sf0124306601 1 24307645 1.32E-15 NA
vg0232755756 sf0232749887 2 32755756 1.46E-15 NA
vg0207925710 sf0207925709 2 7925710 1.67E-15 NA
vg0519715178 sf0519652662 5 19715178 3.00E-15 1.46E-06
vg0518984986 sf0518922470 5 18984986 NA 2.79E-06
vg0519704391 sf0519641875 5 19704391 NA 4.87E-06