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 mr1559 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
vg0216691905 sf0216686035 2 16691905 4.40E-12 3.28E-08
vg0216896614 sf0216890744 2 16896614 2.36E-11 1.88E-08
vg1005364864 sf1005381401 10 5364864 3.99E-09 3.93E-06
vg0808345596 sf0808344600 8 8345596 6.87E-08 1.67E-06
vg0216673711 sf0216667841 2 16673711 1.37E-07 1.69E-06
vg0524244054 sf0524181473 5 24244054 1.55E-07 1.60E-06
vg0922188638 sf0922188157 9 22188638 3.63E-07 2.21E-06
vg0217110472 sf0217104602 2 17110472 8.55E-07 3.37E-06
vg0820888052 sf0820885339 8 20888052 9.90E-07 3.26E-06
vg0300249514 sf0300248514 3 249514 8.00E-06 4.23E-06
vg0614458504 sf0614457505 6 14458504 8.39E-06 6.04E-06
vg0820141762 sf0820139049 8 20141762 NA 3.96E-07
vg0819026111 sf0819023398 8 19026111 NA 1.74E-06