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 mr1924 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
vg1012400207 sf1012329022 10 12400207 8.58E-26 2.45E-06
vg0800035708 sf0800034708 8 35708 1.66E-25 NA
vg0106330759 sf0106329759 1 6330759 1.97E-25 NA
vg0233332438 sf0233326569 2 33332438 2.23E-25 NA
vg1108740309 sf1108734919 11 8740309 3.90E-25 NA
vg0518984986 sf0518922470 5 18984986 1.90E-24 9.97E-07
vg0434570897 sf0434385789 4 34570897 2.60E-24 NA
vg1214656787 sf1214654127 12 14656787 5.43E-23 2.95E-07
vg1116933718 sf1116468597 11 16933718 NA 3.17E-06
vg1219570780 sf1219542250 12 19570780 NA 3.95E-06