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 mr1923 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
vg0331273085 sf0331265970 3 31273085 1.84E-12 2.03E-08
vg1202573797 sf1202572799 12 2573797 1.33E-08 NA
vg1122622039 sf1122155910 11 22622039 2.00E-08 NA
vg0126099360 sf0126098316 1 26099360 2.71E-08 NA
vg0911590178 sf0911589177 9 11590178 3.00E-07 1.15E-06
vg1126856638 sf1126385025 11 26856638 8.24E-07 1.69E-06
vg1108502161 sf1108496771 11 8502161 6.77E-06 NA