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 mr1500 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
vg0130289295 sf0130288250 1 30289295 8.82E-09 9.17E-06
vg1104963383 sf1104959194 11 4963383 1.96E-08 NA
vg1118866204 sf1118400013 11 18866204 4.27E-07 NA
vg0130736687 sf0130735643 1 30736687 1.71E-06 NA
vg0513922749 sf0513865293 5 13922749 2.57E-06 4.37E-06