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 mr1640 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
vg0300249514 sf0300248514 3 249514 8.24E-07 8.24E-07
vg1107375253 sf1107370998 11 7375253 1.84E-06 1.84E-06
vg0433638267 sf0433453150 4 33638267 4.16E-06 4.16E-06
vg0431411704 sf0431226602 4 31411704 4.40E-06 4.41E-06
vg1106375766 sf1106371518 11 6375766 8.84E-06 8.84E-06