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 mr1286 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
vg0406960814 sf0406956082 4 6960814 9.93E-08 1.54E-06
vg0406853946 sf0406849391 4 6853946 4.35E-07 8.64E-07
vg0406707016 sf0406702463 4 6707016 1.30E-06 2.27E-06
vg0715817404 sf0715816411 7 15817404 4.00E-06 5.00E-06
vg1216729892 sf1216723846 12 16729892 5.88E-06 2.94E-06
vg0132161653 sf0132160609 1 32161653 NA 8.77E-07