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 mr1414 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
vg0411323496 sf0411314199 4 11323496 2.73E-08 NA
vg0407717352 sf0407712619 4 7717352 4.75E-08 NA
vg0408471938 sf0408467212 4 8471938 5.83E-08 NA
vg1003198108 sf1003197085 10 3198108 8.63E-08 NA
vg0524716581 sf0524654001 5 24716581 1.50E-07 2.21E-06
vg1210332224 sf1210329637 12 10332224 1.67E-07 4.15E-06