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 mr1836 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
vg0232682520 sf0232676651 2 32682520 7.05E-10 1.31E-06
vg0135619676 sf0135618633 1 35619676 2.25E-09 NA
vg0805018852 sf0805017855 8 5018852 3.79E-09 8.59E-06
vg0139584519 sf0139583476 1 39584519 8.14E-09 NA
vg0620434725 sf0620433728 6 20434725 1.04E-08 NA
vg0817380483 sf0817377769 8 17380483 7.01E-08 2.98E-07
vg0812016141 sf0812015146 8 12016141 4.27E-07 2.47E-06
vg0909177526 sf0909176525 9 9177526 9.02E-07 NA
vg0210675135 sf0210675133 2 10675135 2.22E-06 NA
vg1112981588 sf1112517909 11 12981588 2.95E-06 9.94E-07
vg0800728758 sf0800727758 8 728758 3.00E-06 NA
vg0128867188 sf0128866143 1 28867188 5.56E-06 NA