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 mr1405 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
vg0419118424 sf0418946462 4 19118424 2.13E-07 2.13E-07
vg0820974361 sf0820971648 8 20974361 1.40E-06 1.40E-06
vg1109529985 sf1109524562 11 9529985 1.49E-06 1.49E-06
vg0900901867 sf0900900867 9 901867 1.84E-06 1.84E-06
vg0710985476 sf0710984482 7 10985476 3.29E-06 3.30E-06