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 mr1660 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
vg1218087584 sf1218059020 12 18087584 1.02E-14 1.44E-06
vg0919506914 sf0919506504 9 19506914 8.72E-13 NA
vg0304596104 sf0304595106 3 4596104 1.78E-12 NA
vg0625219859 sf0625218862 6 25219859 1.79E-11 NA
vg0911769544 sf0911768543 9 11769544 4.18E-11 NA
vg0626441347 sf0626440350 6 26441347 1.27E-10 2.42E-07
vg0917310929 sf0917309928 9 17310929 5.58E-10 3.95E-06