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 mr1681 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
vg0324076908 sf0324074987 3 24076908 3.91E-10 3.91E-10
vg0316311631 sf0316310278 3 16311631 2.54E-07 2.54E-07
vg0316685104 sf0316683749 3 16685104 4.22E-07 4.23E-07
vg0140501355 sf0140500312 1 40501355 5.49E-07 5.49E-07
vg0321809303 sf0321807813 3 21809303 9.05E-07 9.06E-07
vg0318055979 sf0318054761 3 18055979 2.45E-06 2.45E-06
vg0706285104 sf0706284107 7 6285104 3.73E-06 3.73E-06