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 mr1651 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
vg1215352883 sf1215350181 12 15352883 1.13E-08 5.82E-07
vg0424051023 sf0423865884 4 24051023 3.27E-08 5.28E-06
vg0916034764 sf0916033763 9 16034764 9.88E-07 4.63E-07
vg1119344818 sf1118878506 11 19344818 1.99E-06 2.83E-06
vg0510928675 sf0510928604 5 10928675 4.53E-06 8.25E-07
vg1217860400 sf1217831834 12 17860400 NA 3.09E-06