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 mr1924 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
vg0106294847 sf0106293847 1 6294847 8.23E-09 6.73E-06
vg0710771920 sf0710770926 7 10771920 1.62E-08 2.71E-06
vg0106330759 sf0106329759 1 6330759 1.70E-08 3.98E-06
vg1106375766 sf1106371518 11 6375766 3.33E-08 6.65E-08
vg0710610393 sf0710609399 7 10610393 3.75E-08 3.84E-07
vg0130290451 sf0130289406 1 30290451 1.71E-07 1.25E-06
vg1116933718 sf1116468597 11 16933718 4.37E-07 1.80E-06
vg0216716710 sf0216710840 2 16716710 3.59E-06 5.18E-06
vg0518984986 sf0518922470 5 18984986 5.40E-06 2.79E-06