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 mr1599 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
vg0216763637 sf0216757767 2 16763637 5.40E-16 8.06E-10
vg0506159272 sf0506159211 5 6159272 3.98E-12 NA
vg1216651011 sf1216644965 12 16651011 5.93E-11 3.18E-06
vg0515732737 sf0515675278 5 15732737 3.30E-10 NA
vg0519916493 sf0519853969 5 19916493 3.49E-10 NA
vg0710453841 sf0710452847 7 10453841 NA 4.63E-06