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 mr1407 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
vg0820796944 sf0820794231 8 20796944 2.67E-06 5.77E-06
vg0726758298 sf0726757304 7 26758298 2.84E-06 NA
vg1204560575 sf1204559563 12 4560575 3.23E-06 4.03E-06
vg1106375766 sf1106371518 11 6375766 3.58E-06 1.36E-06
vg0235128703 sf0235122834 2 35128703 6.10E-06 8.75E-06