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 mr1040 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
vg0433908182 sf0433723078 4 33908182 1.48E-09 1.41E-06
vg0818164413 sf0818161700 8 18164413 2.17E-09 NA
vg0430345493 sf0430160370 4 30345493 5.38E-09 NA
vg0203321613 sf0203321611 2 3321613 1.36E-08 NA
vg0413426647 sf0413417361 4 13426647 2.03E-08 NA
vg1002726149 sf1002725126 10 2726149 9.20E-06 5.47E-07