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 mr1061 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
vg1217551907 sf1217545862 12 17551907 3.22E-07 3.22E-07
vg1008026033 sf1008018204 10 8026033 5.48E-07 5.48E-07
vg0714344926 sf0714343933 7 14344926 1.55E-06 1.55E-06
vg0403565641 sf0403561243 4 3565641 2.12E-06 2.12E-06
vg0421403601 sf0421231654 4 21403601 3.26E-06 3.26E-06
vg0215890449 sf0215884579 2 15890449 3.66E-06 3.66E-06
vg0323811167 sf0323809341 3 23811167 4.04E-06 4.04E-06