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 mr1296 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
vg0813352775 sf0813350330 8 13352775 1.84E-07 4.06E-06
vg0135233075 sf0135232032 1 35233075 2.42E-06 4.60E-06
vg0824561001 sf0824558287 8 24561001 3.39E-06 2.11E-06
vg1104298838 sf1104294740 11 4298838 4.45E-06 3.33E-06
vg0132413637 sf0132412593 1 32413637 8.00E-06 3.03E-06
vg0414281024 sf0414271737 4 14281024 NA 2.38E-07
vg0113688544 sf0113687518 1 13688544 NA 2.70E-06
vg1216759163 sf1216753117 12 16759163 NA 4.87E-06
vg1216759715 sf1216753669 12 16759715 NA 9.43E-06