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
vg0106689613 sf0106688613 1 6689613 3.32E-10 3.32E-10
vg0106679257 sf0106678257 1 6679257 3.52E-10 3.51E-10
vg0224035929 sf0224030060 2 24035929 4.51E-08 4.51E-08
vg0911638105 sf0911637104 9 11638105 4.85E-07 4.85E-07
vg0628103813 sf0628102815 6 28103813 5.46E-07 5.46E-07
vg0105078015 sf0105077015 1 5078015 1.03E-06 1.03E-06
vg0603996692 sf0603995693 6 3996692 1.43E-06 1.43E-06
vg0909867986 sf0909866985 9 9867986 1.52E-06 1.52E-06
vg0105467672 sf0105466672 1 5467672 2.01E-06 2.01E-06
vg0317879120 sf0317877902 3 17879120 4.71E-06 4.71E-06