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 mr1049 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
vg0421031231 sf0420859284 4 21031231 1.40E-06 1.40E-06
vg0816119916 sf0816117202 8 16119916 2.17E-06 2.17E-06
vg1109631523 sf1109626100 11 9631523 2.81E-06 2.81E-06
vg0116961602 sf0116960556 1 16961602 3.31E-06 3.31E-06
vg0623981969 sf0623980972 6 23981969 3.55E-06 3.55E-06
vg0427788963 sf0427603823 4 27788963 3.78E-06 3.78E-06
vg0142903537 sf0142902493 1 42903537 3.79E-06 3.79E-06
vg0424181194 sf0423996055 4 24181194 4.03E-06 4.03E-06
vg0404029438 sf0404025045 4 4029438 4.29E-06 4.29E-06