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 mr1554 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
vg0820968946 sf0820966233 8 20968946 2.08E-08 1.17E-06
vg0119598439 sf0119597394 1 19598439 2.64E-08 6.05E-06
vg0820967861 sf0820965148 8 20967861 4.87E-08 7.85E-07
vg0130351635 sf0130350591 1 30351635 2.66E-07 2.31E-06
vg0820997872 sf0820995159 8 20997872 1.53E-06 3.13E-06
vg0820478740 sf0820476027 8 20478740 8.17E-06 NA