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 mr1048 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
vg0601214799 sf0601213800 6 1214799 1.58E-06 1.58E-06
vg1216729892 sf1216723846 12 16729892 1.68E-06 1.68E-06
vg1117431373 sf1116965228 11 17431373 2.07E-06 2.07E-06
vg0826159919 sf0826157205 8 26159919 2.23E-06 2.23E-06
vg1101529376 sf1101528377 11 1529376 2.75E-06 2.75E-06
vg0826150537 sf0826147823 8 26150537 3.56E-06 3.56E-06
vg0327981236 sf0327974290 3 27981236 4.59E-06 4.59E-06
vg1122446629 sf1121980500 11 22446629 4.63E-06 4.63E-06