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 mr1590 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
vg0418242514 sf0418070560 4 18242514 2.42E-07 2.43E-07
vg0630441706 sf0630440708 6 30441706 8.93E-07 8.94E-07
vg0622817682 sf0622816685 6 22817682 9.46E-07 9.47E-07
vg1118320073 sf1117853931 11 18320073 1.15E-06 1.15E-06
vg0809155982 sf0809154986 8 9155982 1.67E-06 1.67E-06
vg0902272767 sf0902271767 9 2272767 1.92E-06 1.92E-06
vg0908226638 sf0908225638 9 8226638 2.33E-06 2.33E-06
vg0129164752 sf0129163707 1 29164752 3.76E-06 3.76E-06