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 mr1033 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
vg0613474765 sf0613473766 6 13474765 1.85E-97 4.62E-26
vg0613478027 sf0613477028 6 13478027 1.70E-95 1.70E-27
vg0617844295 sf0617843298 6 17844295 2.41E-89 1.59E-19
vg0617841675 sf0617840678 6 17841675 1.76E-87 8.67E-20
vg0620693330 sf0620692333 6 20693330 7.16E-78 NA
vg0613461816 sf0613460817 6 13461816 NA 3.87E-12
vg0621021467 sf0621020470 6 21021467 NA 1.34E-09
vg0613478814 sf0613477815 6 13478814 NA 1.56E-08