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 mr1573 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
vg1114873399 sf1114409713 11 14873399 4.51E-08 3.08E-07
vg0406717258 sf0406712705 4 6717258 4.04E-07 NA
vg0710572692 sf0710571698 7 10572692 4.49E-07 3.07E-07
vg0804653438 sf0804652441 8 4653438 NA 2.06E-06
vg0216417043 sf0216411173 2 16417043 NA 2.25E-06