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 mr1513 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
vg0225285088 sf0225279219 2 25285088 1.16E-06 1.16E-06
vg0908388909 sf0908387909 9 8388909 2.40E-06 2.40E-06
vg1104839489 sf1104835391 11 4839489 2.51E-06 2.51E-06
vg0621705842 sf0621704845 6 21705842 2.88E-06 2.88E-06
vg1104807637 sf1104803539 11 4807637 3.48E-06 3.48E-06
vg0908226638 sf0908225638 9 8226638 4.19E-06 4.19E-06