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 mr1623 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
vg0619755654 sf0619754657 6 19755654 1.27E-08 5.49E-06
vg0415966080 sf0415794113 4 15966080 1.17E-06 4.07E-06
vg0609173263 sf0609172264 6 9173263 1.46E-06 4.98E-06
vg0519198286 sf0519135770 5 19198286 3.85E-06 NA
vg1224600619 sf1224567073 12 24600619 4.47E-06 2.36E-07