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 mr1657 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
vg0523612364 sf0523549785 5 23612364 1.31E-07 3.47E-07
vg0133436043 sf0133434999 1 33436043 5.65E-07 6.15E-07
vg1109558035 sf1109552612 11 9558035 1.52E-06 1.39E-06
vg1226039416 sf1226005810 12 26039416 2.40E-06 4.30E-06
vg0806703463 sf0806702468 8 6703463 4.78E-06 3.92E-06
vg1226065924 sf1226032318 12 26065924 7.51E-06 NA