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 mr1633 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
vg0205284721 sf0205284719 2 5284721 2.50E-17 3.71E-12
vg0205295885 sf0205295883 2 5295885 6.85E-17 1.31E-12
vg1103858928 sf1103854830 11 3858928 2.65E-10 NA
vg0124879589 sf0124878545 1 24879589 2.93E-10 NA
vg0224905791 sf0224899922 2 24905791 5.48E-10 NA
vg0131845730 sf0131844686 1 31845730 6.92E-10 NA
vg0205293173 sf0205293171 2 5293173 2.55E-08 4.33E-08
vg0316679196 sf0316677841 3 16679196 1.03E-06 NA
vg0527033385 sf0526970741 5 27033385 NA 6.80E-06