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 mr1880 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
vg0419769666 sf0419597701 4 19769666 6.89E-14 NA
vg0425010504 sf0424825365 4 25010504 2.04E-13 NA
vg0406062876 sf0406058315 4 6062876 2.74E-13 NA
vg0414202308 sf0414193024 4 14202308 6.04E-13 NA
vg0823106771 sf0823104058 8 23106771 1.07E-11 NA
vg0413295774 sf0413286485 4 13295774 1.86E-10 NA
vg0823871834 sf0823869120 8 23871834 3.79E-10 2.84E-06