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 mr1540 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
vg1017130116 sf1017058888 10 17130116 2.91E-19 1.64E-06
vg1016228567 sf1016157339 10 16228567 7.00E-19 1.22E-06
vg0519755571 sf0519693055 5 19755571 1.18E-17 NA
vg0408057772 sf0408053044 4 8057772 2.40E-17 NA
vg0129868849 sf0129867804 1 29868849 4.66E-17 9.80E-06
vg0132649248 sf0132648204 1 32649248 5.81E-17 NA
vg1002809299 sf1002808276 10 2809299 1.58E-16 3.60E-06