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 mr1743 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
vg0128529665 sf0128528620 1 28529665 6.30E-10 NA
vg0129899993 sf0129898948 1 29899993 1.39E-09 NA
vg0917926619 sf0917925618 9 17926619 1.71E-09 NA
vg0316957285 sf0316956159 3 16957285 2.09E-09 NA
vg0207096735 sf0207096735 2 7096735 3.05E-09 NA
vg1214600105 sf1214597445 12 14600105 2.20E-07 NA
vg0220096466 sf0220090598 2 20096466 8.86E-07 NA
vg0317321849 sf0317320659 3 17321849 3.02E-06 3.87E-06
vg0808100775 sf0808099779 8 8100775 NA 1.49E-06
vg0619886632 sf0619885635 6 19886632 NA 8.24E-06