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 mr1478 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
vg0300353676 sf0300352674 3 353676 1.15E-11 NA
vg0234328298 sf0234322429 2 34328298 2.88E-11 NA
vg0137605963 sf0137604920 1 37605963 2.37E-10 NA
vg0129305001 sf0129303956 1 29305001 3.64E-10 NA
vg0306391946 sf0306390946 3 6391946 5.54E-10 NA
vg0906612050 sf0906611050 9 6612050 3.59E-07 1.45E-06