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 mr1115 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
vg0726964336 sf0726963342 7 26964336 9.15E-12 NA
vg0125460828 sf0125459784 1 25460828 1.37E-11 NA
vg0123684697 sf0123683653 1 23684697 8.05E-11 NA
vg1217426109 sf1217420064 12 17426109 1.51E-10 NA
vg0138427451 sf0138426408 1 38427451 2.27E-10 NA
vg0412512760 sf0412503470 4 12512760 8.49E-09 2.16E-07
vg1220271826 sf1220243268 12 20271826 7.75E-08 4.95E-06
vg0431782557 sf0431597450 4 31782557 5.16E-07 3.79E-06
vg0527925493 sf0527862850 5 27925493 1.91E-06 NA
vg0727206096 sf0727205102 7 27206096 1.94E-06 NA
vg1106375766 sf1106371518 11 6375766 3.80E-06 2.69E-06