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 mr1891 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
vg0715299495 sf0715298502 7 15299495 8.35E-45 NA
vg0713627339 sf0713626346 7 13627339 9.66E-45 4.01E-06
vg0334608078 sf0334600948 3 34608078 1.09E-44 NA
vg0823628585 sf0823625871 8 23628585 2.51E-44 NA
vg1014395173 sf1014323939 10 14395173 3.07E-44 7.91E-06
vg0828386953 sf0828384239 8 28386953 5.53E-44 NA
vg0717017835 sf0717016842 7 17017835 8.37E-44 4.89E-06
vg0909065655 sf0909064654 9 9065655 2.29E-40 2.13E-06
vg0105398179 sf0105397179 1 5398179 6.96E-39 2.41E-06
vg0407785574 sf0407780842 4 7785574 NA 9.75E-08
vg0721382199 sf0721381206 7 21382199 NA 1.32E-06
vg0406950547 sf0406945815 4 6950547 NA 1.91E-06
vg0715756182 sf0715755189 7 15756182 NA 2.89E-06
vg0626042692 sf0626041695 6 26042692 NA 3.18E-06
vg1014284779 sf1014213545 10 14284779 NA 4.23E-06