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 mr1149 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
vg0222739831 sf0222733962 2 22739831 1.17E-50 1.37E-33
vg0223723973 sf0223718104 2 23723973 9.99E-18 6.04E-08
vg0223663745 sf0223657876 2 23663745 2.20E-15 7.87E-09
vg0223077967 sf0223072098 2 23077967 3.43E-15 1.54E-07
vg0224640486 sf0224634617 2 24640486 2.68E-14 2.34E-06
vg1112606104 sf1112142307 11 12606104 2.71E-14 3.01E-06
vg0223556553 sf0223550684 2 23556553 1.53E-13 4.85E-06
vg0224382271 sf0224376402 2 24382271 6.70E-13 3.29E-09
vg0222897004 sf0222891135 2 22897004 2.82E-11 1.01E-07
vg0225400091 sf0225394222 2 25400091 9.99E-11 5.38E-07
vg0222765370 sf0222759501 2 22765370 4.31E-10 5.76E-07
vg0223269173 sf0223263304 2 23269173 2.96E-09 5.69E-07
vg0222680278 sf0222674409 2 22680278 3.12E-09 1.73E-09
vg0300265158 sf0300264158 3 265158 1.49E-07 NA
vg0122682136 sf0122681091 1 22682136 1.63E-07 NA
vg0412476197 sf0412466912 4 12476197 2.93E-07 NA