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 mr1473 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
vg0909815072 sf0909814071 9 9815072 1.14E-06 1.15E-06
vg0804453676 sf0804452679 8 4453676 1.18E-06 1.18E-06
vg0701185368 sf0701184368 7 1185368 1.77E-06 1.78E-06
vg0334841623 sf0334834493 3 34841623 1.98E-06 1.98E-06
vg0903783463 sf0903782463 9 3783463 3.05E-06 3.05E-06
vg1020503467 sf1020431946 10 20503467 3.07E-06 3.08E-06
vg0101289411 sf0101288411 1 1289411 4.30E-06 4.31E-06