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 mr1951 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
vg0106703694 sf0106702694 1 6703694 4.84E-20 5.85E-11
vg0427224260 sf0427039130 4 27224260 4.92E-14 NA
vg0514347110 sf0514289653 5 14347110 1.48E-13 NA
vg0509755928 sf0509755857 5 9755928 1.48E-13 NA
vg0608638903 sf0608637904 6 8638903 8.81E-13 NA
vg0424217937 sf0424032798 4 24217937 2.18E-10 1.39E-06
vg0421520546 sf0421348597 4 21520546 5.75E-10 4.88E-06
vg1126758549 sf1126286936 11 26758549 1.52E-07 6.94E-06
vg1216158559 sf1216155855 12 16158559 NA 1.57E-06