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 mr1464 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
vg0300249514 sf0300248514 3 249514 8.88E-09 8.88E-09
vg0207908595 sf0207908594 2 7908595 2.92E-08 2.92E-08
vg0324205491 sf0324203570 3 24205491 2.42E-07 2.42E-07
vg0819413870 sf0819411157 8 19413870 2.29E-06 2.29E-06
vg1207539985 sf1207537391 12 7539985 3.27E-06 3.27E-06