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 mr1349 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
vg0306313857 sf0306312857 3 6313857 2.89E-15 NA
vg0200456993 sf0200456993 2 456993 5.39E-15 2.69E-06
vg0200456649 sf0200456649 2 456649 5.77E-15 1.84E-06
vg0234397577 sf0234391708 2 34397577 1.59E-14 NA
vg0526156771 sf0526094191 5 26156771 2.54E-14 NA
vg0516684304 sf0516623946 5 16684304 1.01E-13 NA
vg0619807728 sf0619806731 6 19807728 9.03E-13 NA
vg0107647091 sf0107646091 1 7647091 2.52E-12 1.90E-07
vg0920052521 sf0920052040 9 20052521 8.78E-11 NA
vg0434743189 sf0434558081 4 34743189 3.90E-10 NA
vg1108111871 sf1108107616 11 8111871 NA 1.67E-06
vg0528736705 sf0528674060 5 28736705 NA 2.32E-06