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 mr1921 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
vg0205285714 sf0205285712 2 5285714 1.07E-18 2.33E-10
vg0205287313 sf0205287311 2 5287313 6.04E-18 1.51E-10
vg1214656787 sf1214654127 12 14656787 4.37E-11 1.92E-07
vg0205035629 sf0205035626 2 5035629 5.69E-11 NA
vg0138523638 sf0138522595 1 38523638 9.69E-11 NA
vg1012827616 sf1012756431 10 12827616 9.77E-11 NA
vg0518984986 sf0518922470 5 18984986 1.90E-08 7.31E-07