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 mr1981 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
vg0430882025 sf0430696903 4 30882025 8.39E-09 8.39E-09
vg0316509974 sf0316508619 3 16509974 2.07E-06 2.07E-06
vg1126095799 sf1125624213 11 26095799 2.40E-06 2.40E-06
vg0110904486 sf0110903462 1 10904486 2.42E-06 2.42E-06
vg0618214950 sf0618213953 6 18214950 2.68E-06 2.68E-06
vg0714395075 sf0714394082 7 14395075 3.21E-06 3.21E-06
vg1122617347 sf1122151218 11 22617347 3.48E-06 3.48E-06