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 mr1245 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
vg0527656990 sf0527594347 5 27656990 1.39E-07 7.23E-07
vg0505850932 sf0505850870 5 5850932 1.47E-07 8.93E-08
vg0611290898 sf0611289899 6 11290898 5.19E-07 4.43E-06
vg0624805039 sf0624804042 6 24805039 1.68E-06 6.26E-06
vg1206605318 sf1206604208 12 6605318 4.59E-06 1.49E-06
vg0714723264 sf0714722271 7 14723264 NA 4.61E-06