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 mr1208 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
vg0901360162 sf0901359162 9 1360162 1.05E-06 1.05E-06
vg1002966355 sf1002965332 10 2966355 1.43E-06 1.43E-06
vg0514934001 sf0514876544 5 14934001 2.06E-06 2.06E-06
vg1004557601 sf1004574139 10 4557601 2.42E-06 2.42E-06
vg0126439526 sf0126438482 1 26439526 2.99E-06 2.99E-06