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 mr1444 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
vg0917631772 sf0917630771 9 17631772 4.15E-07 4.15E-07
vg0140479397 sf0140478354 1 40479397 1.25E-06 1.25E-06
vg0131964524 sf0131963480 1 31964524 1.86E-06 1.86E-06
vg0407000775 sf0406996046 4 7000775 3.17E-06 3.17E-06
vg0407954232 sf0407883204 4 7954232 3.23E-06 3.23E-06
vg1117514629 sf1117048484 11 17514629 3.88E-06 3.89E-06
vg0522869754 sf0522807196 5 22869754 4.50E-06 4.50E-06