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 mr1972 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
vg0406715803 sf0406711250 4 6715803 1.76E-06 1.45E-06
vg0715481027 sf0715480034 7 15481027 5.90E-06 1.48E-06
vg1002941211 sf1002940188 10 2941211 NA 1.54E-06
vg0216380020 sf0216374150 2 16380020 NA 1.92E-06
vg0406860866 sf0406856311 4 6860866 NA 3.04E-06
vg0141859911 sf0141858868 1 41859911 NA 4.31E-06
vg0414510575 sf0414501289 4 14510575 NA 8.31E-06