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 mr1223 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
vg1115442463 sf1114978775 11 15442463 1.41E-07 4.19E-06
vg0216528446 sf0216522576 2 16528446 2.51E-07 3.27E-07
vg0823243074 sf0823240361 8 23243074 4.27E-07 NA
vg1115480914 sf1115017227 11 15480914 8.52E-07 8.02E-07
vg1111107806 sf1111102123 11 11107806 8.89E-07 3.04E-06
vg0335447088 sf0335439957 3 35447088 1.99E-06 1.87E-06
vg0335540142 sf0335533011 3 35540142 5.60E-06 1.71E-06
vg0103395450 sf0103394450 1 3395450 7.28E-06 NA