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 mr1649 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
vg1005431953 sf1005448490 10 5431953 1.00E-16 NA
vg1225551362 sf1225517757 12 25551362 1.87E-16 NA
vg1226750394 sf1226716792 12 26750394 2.60E-16 2.59E-06
vg0327439642 sf0327432695 3 27439642 2.73E-16 NA
vg1013484812 sf1013413582 10 13484812 3.76E-16 NA
vg0330989296 sf0330982183 3 30989296 9.41E-16 NA
vg0826158844 sf0826156130 8 26158844 3.17E-12 4.34E-08
vg0826158875 sf0826156161 8 26158875 3.35E-12 4.73E-08
vg0107385646 sf0107384646 1 7385646 5.71E-12 NA
vg0216621262 sf0216615392 2 16621262 NA 3.56E-08
vg0216625219 sf0216619349 2 16625219 NA 1.59E-07
vg0327447631 sf0327440684 3 27447631 NA 3.83E-07
vg0216732533 sf0216726663 2 16732533 NA 1.60E-06
vg1016933579 sf1016862351 10 16933579 NA 2.08E-06
vg0826161775 sf0826159061 8 26161775 NA 4.03E-06
vg0907797131 sf0907796131 9 7797131 NA 4.40E-06
vg1005678285 sf1005694823 10 5678285 NA 4.45E-06