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 mr1803 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
vg0222035625 sf0222029756 2 22035625 7.54E-07 7.54E-07
vg0206207021 sf0206207021 2 6207021 8.03E-07 8.03E-07
vg1124423034 sf1123956874 11 24423034 1.35E-06 1.35E-06
vg0112185618 sf0112184592 1 12185618 2.75E-06 2.75E-06
vg0706489091 sf0706488096 7 6489091 3.60E-06 3.60E-06
vg1121970827 sf1121504698 11 21970827 3.76E-06 3.76E-06
vg0519456069 sf0519393553 5 19456069 6.83E-06 6.83E-06