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 mr1186 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
vg1214940906 sf1214938248 12 14940906 1.16E-09 4.95E-06
vg0128334522 sf0128333478 1 28334522 7.04E-09 NA
vg0624901650 sf0624900653 6 24901650 1.41E-07 8.33E-06
vg1214944691 sf1214942033 12 14944691 2.87E-07 NA
vg0210265227 sf0210265225 2 10265227 2.14E-06 4.51E-06
vg0216760168 sf0216754298 2 16760168 3.14E-06 8.33E-06