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 mr1765 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
vg0334980357 sf0334973227 3 34980357 4.37E-08 4.37E-08
vg1012891999 sf1012820814 10 12891999 1.47E-07 1.47E-07
vg0820968946 sf0820966233 8 20968946 9.70E-07 9.70E-07
vg0719725023 sf0719724030 7 19725023 2.95E-06 2.95E-06
vg0304365624 sf0304364626 3 4365624 3.47E-06 3.47E-06
vg0334732696 sf0334725566 3 34732696 3.97E-06 3.97E-06