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 mr1474 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
vg0300306966 sf0300305964 3 306966 5.04E-09 NA
vg0306142106 sf0306141106 3 6142106 7.69E-08 3.54E-06
vg0141746853 sf0141745810 1 41746853 9.68E-08 NA
vg1208270538 sf1208267943 12 8270538 1.11E-07 2.84E-06
vg0137230062 sf0137229019 1 37230062 1.17E-06 NA