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 mr1706 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 7.62E-11 NA
vg0123684776 sf0123683732 1 23684776 2.13E-10 NA
vg0141767331 sf0141766288 1 41767331 2.18E-10 NA
vg0141829519 sf0141828476 1 41829519 4.91E-10 NA
vg0205292054 sf0205292052 2 5292054 7.39E-10 1.03E-06
vg1020582981 sf1020511460 10 20582981 3.23E-09 NA
vg0714622950 sf0714621957 7 14622950 4.89E-07 2.17E-06
vg1000467020 sf1000465996 10 467020 5.58E-06 NA