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 mr1567 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
vg0724512930 sf0724511936 7 24512930 6.56E-15 1.33E-11
vg0724529234 sf0724528240 7 24529234 2.01E-14 5.87E-11
vg0103093065 sf0103092065 1 3093065 3.50E-10 NA
vg0528282420 sf0528219775 5 28282420 8.10E-10 6.25E-06
vg0620772016 sf0620771019 6 20772016 3.71E-08 4.73E-06
vg0325213731 sf0325211812 3 25213731 5.16E-08 NA
vg0316689752 sf0316688398 3 16689752 2.28E-07 NA
vg1106872087 sf1106867832 11 6872087 4.88E-07 7.10E-07
vg1106670187 sf1106665940 11 6670187 2.12E-06 2.90E-06
vg0724492608 sf0724491614 7 24492608 NA 1.89E-07
vg0716888581 sf0716887588 7 16888581 NA 4.16E-06