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 mr1958 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
vg0110462691 sf0110461667 1 10462691 6.80E-07 6.78E-07
vg0306142106 sf0306141106 3 6142106 1.33E-06 1.32E-06
vg0527372826 sf0527310182 5 27372826 1.95E-06 1.95E-06
vg0306324522 sf0306323522 3 6324522 4.51E-06 4.51E-06
vg0528653684 sf0528591039 5 28653684 4.69E-06 4.68E-06