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 mr1916 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
vg0106679257 sf0106678257 1 6679257 7.53E-17 1.60E-15
vg0317879120 sf0317877902 3 17879120 4.46E-09 6.51E-07
vg0105459915 sf0105458915 1 5459915 1.61E-06 1.30E-06
vg0413191246 sf0413181956 4 13191246 2.08E-06 1.07E-06
vg0817496643 sf0817493929 8 17496643 9.19E-06 3.89E-06