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 mr1712 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
vg0231867258 sf0231861389 2 31867258 8.28E-09 1.06E-08
vg0433705748 sf0433520630 4 33705748 9.69E-09 1.05E-06
vg0500807732 sf0500807714 5 807732 3.80E-07 4.83E-08
vg1010454306 sf1010383127 10 10454306 1.27E-06 4.55E-06
vg0614471183 sf0614470184 6 14471183 NA 1.05E-06
vg0617122838 sf0617121841 6 17122838 NA 1.51E-06
vg0525530914 sf0525468335 5 25530914 NA 1.75E-06