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 mr1715 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
vg0405986129 sf0405981569 4 5986129 4.20E-18 NA
vg0726939781 sf0726938787 7 26939781 4.27E-18 NA
vg0423147772 sf0422962627 4 23147772 6.46E-18 NA
vg0235123893 sf0235118024 2 35123893 2.22E-17 NA
vg1103051950 sf1103047854 11 3051950 4.84E-17 NA
vg0907386916 sf0907385916 9 7386916 5.27E-11 NA
vg1225862470 sf1225828865 12 25862470 NA 9.36E-07