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 mr1029 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
vg0522473219 sf0522410661 5 22473219 3.26E-06 3.56E-06
vg0916243238 sf0916242237 9 16243238 9.42E-06 2.01E-06
vg0121834497 sf0121833452 1 21834497 NA 2.31E-06
vg0410180309 sf0410171006 4 10180309 NA 4.27E-06
vg0500333113 sf0500333113 5 333113 NA 8.18E-06