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 mr1866 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
vg0726714837 sf0726713843 7 26714837 3.37E-22 1.69E-06
vg0726726990 sf0726725996 7 26726990 1.21E-21 2.71E-06
vg0825340856 sf0825338142 8 25340856 1.49E-20 4.33E-06
vg0310368348 sf0310367264 3 10368348 7.01E-20 NA
vg0805964617 sf0805963620 8 5964617 9.53E-20 NA
vg1215382439 sf1215379737 12 15382439 2.99E-19 NA
vg0413768748 sf0413759462 4 13768748 1.33E-16 5.46E-07
vg0413764976 sf0413755690 4 13764976 NA 9.25E-13
vg1215652345 sf1215649642 12 15652345 NA 9.92E-08
vg0416149416 sf0415977449 4 16149416 NA 9.13E-07
vg1125281259 sf1124815099 11 25281259 NA 1.47E-06
vg0217637634 sf0217631764 2 17637634 NA 2.11E-06
vg1109865325 sf1109859902 11 9865325 NA 4.22E-06
vg0317321849 sf0317320659 3 17321849 NA 4.74E-06