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 mr1579 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
vg0208756843 sf0208756842 2 8756843 2.40E-08 5.74E-06
vg1217795376 sf1217766810 12 17795376 3.59E-08 NA
vg0208707423 sf0208707422 2 8707423 3.87E-08 9.95E-06
vg1215163870 sf1215161206 12 15163870 6.76E-08 8.56E-06
vg1215222085 sf1215219382 12 15222085 3.54E-07 2.25E-06
vg0800334326 sf0800333326 8 334326 3.69E-07 4.42E-06
vg1215612687 sf1215609984 12 15612687 7.01E-07 1.89E-06
vg0912341424 sf0912340423 9 12341424 1.86E-06 NA
vg1215325180 sf1215322478 12 15325180 7.83E-06 2.75E-06
vg0713465183 sf0713464190 7 13465183 9.64E-06 4.68E-06
vg0819321674 sf0819318961 8 19321674 NA 3.70E-06