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 mr1511 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
vg0128900932 sf0128899887 1 28900932 7.35E-10 1.68E-06
vg0131768442 sf0131767398 1 31768442 1.12E-09 NA
vg0129297761 sf0129296716 1 29297761 1.36E-09 4.97E-06
vg0922325761 sf0922325280 9 22325761 1.65E-09 NA
vg0303228694 sf0303227690 3 3228694 1.96E-08 NA
vg0808836774 sf0808835778 8 8836774 2.01E-08 NA
vg0821970212 sf0821967499 8 21970212 2.03E-07 1.89E-07
vg0131535738 sf0131534694 1 31535738 NA 8.87E-07
vg0128866915 sf0128865870 1 28866915 NA 1.85E-06