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 mr1960 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
vg0622673582 sf0622672585 6 22673582 1.40E-07 2.87E-06
vg1214134657 sf1214131997 12 14134657 1.65E-06 2.25E-06
vg1219845187 sf1219816657 12 19845187 8.58E-06 NA
vg1214656787 sf1214654127 12 14656787 NA 7.59E-08
vg0527924474 sf0527861831 5 27924474 NA 3.27E-06
vg0400387960 sf0400386958 4 387960 NA 3.84E-06
vg0400132474 sf0400131474 4 132474 NA 8.39E-06
vg0412436211 sf0412426925 4 12436211 NA 9.71E-06