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 mr1744 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
vg0615249086 sf0615248087 6 15249086 1.93E-20 1.21E-06
vg0724529284 sf0724528290 7 24529284 2.75E-19 NA
vg0917582131 sf0917581130 9 17582131 4.66E-19 NA
vg1017965734 sf1017894506 10 17965734 5.58E-19 NA
vg1013366855 sf1013295625 10 13366855 5.68E-19 NA
vg0205031937 sf0205031934 2 5031937 NA 1.25E-06
vg1215609580 sf1215606877 12 15609580 NA 4.50E-06
vg0400897236 sf0400896236 4 897236 NA 5.35E-06