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 mr1423 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
vg0216732365 sf0216726495 2 16732365 1.26E-15 5.81E-08
vg0502983578 sf0502983554 5 2983578 9.06E-11 NA
vg0201099179 sf0201099179 2 1099179 9.60E-11 NA
vg0505554444 sf0505554382 5 5554444 2.34E-10 NA
vg0503021903 sf0503021879 5 3021903 3.92E-10 6.53E-06