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
vg0139783926 sf0139782883 1 39783926 1.53E-10 NA
vg0820850557 sf0820847844 8 20850557 1.06E-08 NA
vg0728114135 sf0728113142 7 28114135 2.06E-08 NA
vg0125510468 sf0125509424 1 25510468 2.42E-08 NA
vg0619791673 sf0619790676 6 19791673 5.53E-08 NA
vg0709128655 sf0709127661 7 9128655 2.49E-07 1.38E-06
vg0808210049 sf0808209053 8 8210049 3.03E-07 2.87E-07
vg0209114822 sf0209114820 2 9114822 1.58E-06 NA
vg0409861930 sf0409852628 4 9861930 2.51E-06 8.96E-07
vg0709322762 sf0709321768 7 9322762 NA 3.72E-06