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 mr1452 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
vg0903736728 sf0903735728 9 3736728 6.00E-07 6.00E-07
vg1122446629 sf1121980500 11 22446629 6.97E-07 6.97E-07
vg0129130509 sf0129129464 1 29130509 1.50E-06 1.50E-06
vg1207248243 sf1207245650 12 7248243 4.43E-06 4.43E-06
vg1104315941 sf1104311843 11 4315941 4.55E-06 4.55E-06
vg0407000775 sf0406996046 4 7000775 7.87E-06 7.87E-06