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 mr1373 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
vg0505514888 sf0505514826 5 5514888 1.43E-08 3.14E-06
vg0820097251 sf0820094538 8 20097251 2.27E-08 NA
vg0510469122 sf0510469051 5 10469122 4.32E-08 NA
vg0112317208 sf0112316182 1 12317208 4.84E-08 8.29E-06
vg0524655448 sf0524592868 5 24655448 5.03E-08 NA
vg0505864665 sf0505864603 5 5864665 2.70E-07 1.93E-07
vg0504756490 sf0504756467 5 4756490 5.68E-07 NA
vg0505677328 sf0505677266 5 5677328 NA 2.03E-06
vg0505632591 sf0505632529 5 5632591 NA 3.20E-06
vg0505593631 sf0505593569 5 5593631 NA 3.53E-06