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 mr1947 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
vg0906443883 sf0906442883 9 6443883 2.41E-07 2.41E-07
vg0906525065 sf0906524065 9 6525065 2.59E-07 2.59E-07
vg0708983069 sf0708982075 7 8983069 3.27E-06 3.27E-06
vg0431411704 sf0431226602 4 31411704 3.93E-06 3.93E-06
vg0322563907 sf0322562396 3 22563907 4.82E-06 4.82E-06
vg0502095253 sf0502095235 5 2095253 9.02E-06 9.02E-06