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 mr1282 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
vg1214688591 sf1214685930 12 14688591 2.69E-15 2.55E-07
vg0819829527 sf0819826814 8 19829527 2.61E-14 2.74E-06
vg0919855604 sf0919855123 9 19855604 2.64E-14 7.38E-07
vg0132364610 sf0132363566 1 32364610 5.85E-14 NA
vg0430611390 sf0430426265 4 30611390 6.89E-14 NA
vg1203657863 sf1203656862 12 3657863 1.70E-13 2.14E-06
vg0223561709 sf0223555840 2 23561709 1.79E-13 4.51E-07
vg0803654150 sf0803653153 8 3654150 3.57E-13 4.63E-06
vg0134272325 sf0134271282 1 34272325 7.43E-13 3.21E-07
vg0618478687 sf0618477690 6 18478687 3.62E-12 5.72E-07
vg0814576026 sf0814573312 8 14576026 2.64E-11 2.85E-06
vg1219779242 sf1219750712 12 19779242 8.95E-11 3.17E-07
vg1104909930 sf1104905741 11 4909930 6.43E-10 2.68E-06
vg0803657241 sf0803656244 8 3657241 NA 1.45E-07
vg0709955551 sf0709954557 7 9955551 NA 8.40E-07
vg0618864422 sf0618863425 6 18864422 NA 2.36E-06
vg0329190894 sf0329183946 3 29190894 NA 3.50E-06