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 mr1501 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
vg1124660528 sf1124194368 11 24660528 5.69E-07 5.69E-07
vg1117596580 sf1117130437 11 17596580 1.89E-06 1.89E-06
vg1012242711 sf1012171526 10 12242711 3.72E-06 3.72E-06
vg0336260325 sf0336253195 3 36260325 3.78E-06 3.78E-06
vg0210290709 sf0210290707 2 10290709 3.85E-06 3.85E-06
vg0620348476 sf0620347479 6 20348476 4.39E-06 4.39E-06
vg0909170084 sf0909169083 9 9170084 4.56E-06 4.56E-06