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 mr1943 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
vg0106296081 sf0106295081 1 6296081 5.05E-38 2.87E-08
vg0106330759 sf0106329759 1 6330759 6.46E-38 3.62E-09
vg0434567760 sf0434382652 4 34567760 5.70E-31 NA
vg0434389908 sf0434204802 4 34389908 9.33E-31 2.17E-06
vg0130351635 sf0130350591 1 30351635 3.87E-30 NA
vg0621192723 sf0621191726 6 21192723 5.35E-30 NA
vg0820888052 sf0820885339 8 20888052 6.59E-30 NA
vg0518984986 sf0518922470 5 18984986 1.05E-24 1.04E-06
vg0505449752 sf0505449730 5 5449752 NA 4.75E-07
vg0106598597 sf0106597597 1 6598597 NA 8.46E-07
vg1214656787 sf1214654127 12 14656787 NA 1.68E-06
vg0200528076 sf0200528076 2 528076 NA 2.97E-06
vg0525550165 sf0525487586 5 25550165 NA 3.77E-06
vg1208634025 sf1208631432 12 8634025 NA 4.09E-06
vg0810665700 sf0810664704 8 10665700 NA 4.34E-06
vg0819961570 sf0819958857 8 19961570 NA 4.57E-06