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 mr1951 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
vg0106803188 sf0106802188 1 6803188 1.09E-11 2.28E-11
vg0616984615 sf0616983618 6 16984615 7.06E-08 2.95E-06
vg0616731072 sf0616730074 6 16731072 8.51E-08 2.73E-06
vg1003557200 sf1003556177 10 3557200 3.96E-06 4.47E-06
vg0414098617 sf0414089332 4 14098617 NA 1.05E-06
vg0215664387 sf0215658517 2 15664387 NA 1.81E-06