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 mr1379 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
vg0216641844 sf0216635974 2 16641844 2.05E-12 4.75E-09
vg0216760157 sf0216754287 2 16760157 3.06E-12 3.49E-09
vg1005364864 sf1005381401 10 5364864 1.56E-08 3.44E-06
vg0214744055 sf0214738185 2 14744055 1.55E-07 4.20E-06
vg0217110472 sf0217104602 2 17110472 2.30E-07 1.26E-06
vg0606310477 sf0606309478 6 6310477 2.49E-07 4.04E-07
vg0808345596 sf0808344600 8 8345596 3.25E-07 2.01E-06
vg0610114799 sf0610113800 6 10114799 5.41E-07 3.69E-06
vg0217737908 sf0217732038 2 17737908 8.75E-07 2.26E-06
vg0820816962 sf0820814249 8 20816962 8.79E-07 NA
vg0820141762 sf0820139049 8 20141762 NA 1.34E-06
vg0327336374 sf0327329427 3 27336374 NA 2.34E-06