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 mr1025 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 1.95E-07 1.95E-07
vg0820974361 sf0820971648 8 20974361 1.09E-06 1.09E-06
vg0820888052 sf0820885339 8 20888052 1.67E-06 1.67E-06
vg1109530326 sf1109524903 11 9530326 1.95E-06 1.95E-06
vg1104978992 sf1104974803 11 4978992 2.32E-06 2.32E-06
vg0431655631 sf0431470524 4 31655631 2.65E-06 2.65E-06
vg0718838390 sf0718837397 7 18838390 2.65E-06 2.65E-06
vg1109631523 sf1109626100 11 9631523 4.37E-06 4.37E-06
vg1214822308 sf1214819649 12 14822308 4.76E-06 4.76E-06