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 mr1403 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
vg1216602480 sf1216599773 12 16602480 6.11E-10 8.52E-06
vg0800293632 sf0800292632 8 293632 3.61E-09 1.54E-07
vg0820421110 sf0820418397 8 20421110 4.13E-09 NA
vg0108674689 sf0108673689 1 8674689 4.77E-09 NA
vg0115329766 sf0115328740 1 15329766 3.30E-08 NA
vg0709984451 sf0709983457 7 9984451 1.04E-07 2.28E-07
vg0421407009 sf0421235062 4 21407009 NA 4.28E-06