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 mr1578 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
vg0623833223 sf0623832226 6 23833223 2.16E-06 2.16E-06
vg0900108422 sf0900107422 9 108422 2.76E-06 2.76E-06
vg0316394110 sf0316392755 3 16394110 3.34E-06 3.34E-06
vg0334859866 sf0334852736 3 34859866 3.43E-06 3.43E-06
vg0314984758 sf0314983405 3 14984758 4.24E-06 4.24E-06
vg0506942006 sf0506941948 5 6942006 4.84E-06 4.84E-06
vg0314970214 sf0314968861 3 14970214 6.20E-06 6.20E-06