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 mr1693 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
vg1126873437 sf1126401824 11 26873437 1.67E-06 1.67E-06
vg1117147805 sf1116681657 11 17147805 1.71E-06 1.71E-06
vg0427270986 sf0427085855 4 27270986 1.76E-06 1.76E-06
vg0628503840 sf0628502842 6 28503840 3.32E-06 3.32E-06
vg0825980691 sf0825977977 8 25980691 3.90E-06 3.90E-06
vg1116647697 sf1116182575 11 16647697 4.75E-06 4.75E-06
vg1117147454 sf1116681306 11 17147454 7.65E-06 7.65E-06