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 mr1479 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
vg0226791306 sf0226785437 2 26791306 2.69E-10 NA
vg0424413781 sf0424228642 4 24413781 4.74E-10 NA
vg0226753616 sf0226747747 2 26753616 5.93E-10 1.09E-06
vg0711410816 sf0711409822 7 11410816 6.49E-10 NA
vg0234396710 sf0234390841 2 34396710 8.75E-10 NA
vg0142015207 sf0142014164 1 42015207 9.60E-10 NA
vg0316269128 sf0316267775 3 16269128 1.86E-08 NA
vg0124363805 sf0124362761 1 24363805 2.51E-08 NA
vg0234397294 sf0234391425 2 34397294 4.62E-08 NA
vg0226817183 sf0226811314 2 26817183 2.65E-07 1.00E-06