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 mr1593 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
vg0507070828 sf0507070770 5 7070828 4.67E-39 1.49E-16
vg0507073995 sf0507073937 5 7073995 4.96E-39 1.07E-16
vg0511479803 sf0511479733 5 11479803 1.77E-23 NA
vg0520415809 sf0520353281 5 20415809 6.93E-22 NA
vg0129473674 sf0129472629 1 29473674 1.48E-20 NA
vg0614297874 sf0614296875 6 14297874 1.59E-20 NA
vg0129388746 sf0129387701 1 29388746 1.87E-17 1.79E-06
vg0205280160 sf0205280157 2 5280160 NA 1.15E-06
vg1110845401 sf1110839718 11 10845401 NA 1.21E-06
vg0507123656 sf0507123598 5 7123656 NA 1.35E-06