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 mr1492 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
vg1117584893 sf1117118750 11 17584893 1.97E-08 1.97E-08
vg1202404267 sf1202403268 12 2404267 1.57E-07 1.57E-07
vg0114539233 sf0114538207 1 14539233 1.86E-06 1.86E-06
vg0524983984 sf0524921399 5 24983984 2.05E-06 2.05E-06
vg0526063526 sf0526000946 5 26063526 2.81E-06 2.82E-06
vg0522014819 sf0521952261 5 22014819 2.90E-06 2.90E-06
vg0305410035 sf0305409035 3 5410035 2.98E-06 2.98E-06
vg0206761761 sf0206761761 2 6761761 4.03E-06 4.03E-06
vg0114539569 sf0114538543 1 14539569 4.41E-06 4.41E-06
vg0329248379 sf0329241431 3 29248379 4.49E-06 4.49E-06