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 mr1967 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
vg0431515534 sf0431330433 4 31515534 1.07E-06 1.07E-06
vg1214822308 sf1214819649 12 14822308 1.22E-06 1.22E-06
vg0200528076 sf0200528076 2 528076 1.24E-06 1.24E-06
vg0431750098 sf0431564990 4 31750098 1.46E-06 1.46E-06
vg0627911377 sf0627910379 6 27911377 1.52E-06 1.52E-06
vg1214600105 sf1214597445 12 14600105 2.50E-06 2.50E-06
vg0203000556 sf0203000554 2 3000556 4.79E-06 4.79E-06