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 mr1494 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
vg0819679743 sf0819677030 8 19679743 6.06E-07 4.36E-06
vg0223955910 sf0223950041 2 23955910 1.78E-06 NA
vg0807847137 sf0807846141 8 7847137 4.45E-06 2.15E-06
vg0231688782 sf0231682913 2 31688782 8.31E-06 2.67E-06
vg0714301117 sf0714300124 7 14301117 NA 2.56E-06