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 mr1338 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
vg0336065470 sf0336058399 3 36065470 1.70E-10 NA
vg1212235531 sf1212232869 12 12235531 1.97E-10 NA
vg0119405773 sf0119404728 1 19405773 6.13E-10 NA
vg1221739812 sf1221706359 12 21739812 6.52E-10 NA
vg0202488595 sf0202488593 2 2488595 6.87E-10 NA
vg0800248339 sf0800247339 8 248339 8.85E-10 2.72E-06
vg0729240175 sf0729239183 7 29240175 7.91E-09 NA
vg1125867297 sf1125401216 11 25867297 9.25E-08 NA
vg1112988477 sf1112524798 11 12988477 2.50E-07 1.59E-06