\

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 mr1802 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
vg0307680956 sf0307679894 3 7680956 5.54E-07 5.54E-07
vg0706623534 sf0706622539 7 6623534 1.24E-06 1.24E-06
vg0522311777 sf0522249218 5 22311777 1.50E-06 1.50E-06
vg0916411959 sf0916410958 9 16411959 3.28E-06 3.28E-06
vg0808934061 sf0808933065 8 8934061 4.78E-06 4.78E-06