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 mr1855 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
vg0217093461 sf0217087591 2 17093461 2.58E-101 3.84E-49
vg1220336317 sf1220307759 12 20336317 3.12E-36 2.98E-12
vg1108225523 sf1108220133 11 8225523 5.20E-34 NA
vg1015182556 sf1015111324 10 15182556 6.22E-31 2.53E-07
vg1216728800 sf1216722754 12 16728800 2.07E-26 1.37E-11
vg1103133067 sf1103128970 11 3133067 8.97E-26 6.19E-07
vg1005364284 sf1005380821 10 5364284 4.11E-22 1.93E-06
vg1226816132 sf1226782531 12 26816132 2.44E-19 4.21E-07
vg0212043326 sf0212043322 2 12043326 2.72E-18 4.69E-11
vg0216134526 sf0216128656 2 16134526 5.31E-16 9.99E-12
vg0217116568 sf0217110698 2 17116568 6.85E-16 2.32E-07
vg0710676728 sf0710675734 7 10676728 4.11E-15 3.52E-06
vg0216409820 sf0216403950 2 16409820 7.51E-13 2.74E-07
vg0218261094 sf0218255225 2 18261094 3.26E-12 2.32E-06
vg0216627913 sf0216622043 2 16627913 4.49E-12 7.33E-13
vg0218591450 sf0218585581 2 18591450 2.82E-11 1.20E-06
vg1109924210 sf1109918787 11 9924210 NA 5.67E-07
vg0216412723 sf0216406853 2 16412723 NA 4.90E-06