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 mr1566 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
vg1123677787 sf1123211657 11 23677787 6.92E-07 6.93E-07
vg0910545467 sf0910544466 9 10545467 8.08E-07 8.08E-07
vg0223473843 sf0223467974 2 23473843 1.48E-06 1.48E-06
vg0810506618 sf0810505622 8 10506618 3.17E-06 3.17E-06
vg1124468452 sf1124002292 11 24468452 3.23E-06 3.23E-06
vg0208194726 sf0208194725 2 8194726 8.48E-06 8.48E-06