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 mr1551 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
vg0608135057 sf0608134058 6 8135057 1.40E-29 3.02E-06
vg0607934967 sf0607933968 6 7934967 3.34E-29 3.53E-07
vg0607981292 sf0607980293 6 7981292 1.87E-28 4.53E-07
vg0819975886 sf0819973173 8 19975886 1.68E-26 1.49E-07
vg0708259470 sf0708258475 7 8259470 8.81E-26 NA
vg0421031231 sf0420859284 4 21031231 1.19E-25 NA
vg0719357272 sf0719356279 7 19357272 2.69E-25 NA
vg0819998404 sf0819995691 8 19998404 NA 1.51E-07
vg0513969126 sf0513911670 5 13969126 NA 1.89E-06
vg0421497707 sf0421325758 4 21497707 NA 2.37E-06
vg0706963303 sf0706962308 7 6963303 NA 3.29E-06
vg0815304114 sf0815301400 8 15304114 NA 4.61E-06
vg0515111882 sf0515054424 5 15111882 NA 8.88E-06