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 mr1473 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
vg0231417061 sf0231411192 2 31417061 1.95E-07 1.95E-07
vg1218430770 sf1218402206 12 18430770 1.19E-06 1.19E-06
vg0401249456 sf0401245006 4 1249456 2.45E-06 2.45E-06
vg0630627914 sf0630626916 6 30627914 2.58E-06 2.58E-06
vg1208264724 sf1208262129 12 8264724 3.48E-06 3.48E-06
vg0714475265 sf0714474272 7 14475265 3.51E-06 3.51E-06
vg0208973550 sf0208973548 2 8973550 3.77E-06 3.77E-06
vg1214415351 sf1214412692 12 14415351 4.06E-06 4.06E-06