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 mr1596 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
vg0424045979 sf0423860840 4 24045979 2.30E-09 NA
vg0400287930 sf0400286930 4 287930 3.23E-09 NA
vg0901762072 sf0901761072 9 1762072 3.83E-09 8.47E-06
vg0428761895 sf0428576746 4 28761895 5.42E-09 NA
vg0723551233 sf0723550240 7 23551233 8.83E-09 NA
vg0223074046 sf0223068177 2 23074046 9.09E-09 4.69E-06
vg0316513657 sf0316512302 3 16513657 2.45E-06 6.31E-06