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 mr1431 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
vg0125460621 sf0125459577 1 25460621 5.97E-11 NA
vg0128497255 sf0128496210 1 28497255 7.85E-10 NA
vg0123690615 sf0123689571 1 23690615 1.14E-09 NA
vg1104979071 sf1104974882 11 4979071 2.90E-09 NA
vg0431614108 sf0431429003 4 31614108 1.96E-08 2.62E-06
vg0431655631 sf0431470524 4 31655631 1.97E-08 7.11E-07
vg0709984451 sf0709983457 7 9984451 1.96E-07 6.01E-06
vg0125343772 sf0125342728 1 25343772 1.05E-06 NA
vg1106375766 sf1106371518 11 6375766 1.89E-06 9.41E-07
vg1116933718 sf1116468597 11 16933718 2.24E-06 4.25E-06
vg1127006456 sf1126534843 11 27006456 4.27E-06 NA