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 mr1446 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
vg0107647091 sf0107646091 1 7647091 2.45E-08 9.51E-09
vg0430779487 sf0430594360 4 30779487 3.28E-08 6.17E-06
vg1221121568 sf1221088118 12 21121568 6.46E-08 NA
vg0127410771 sf0127409727 1 27410771 2.15E-07 1.46E-06
vg1020411439 sf1020339918 10 20411439 2.19E-07 NA
vg0224674766 sf0224668897 2 24674766 5.86E-06 NA