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 mr1298 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
vg0314567314 sf0314566001 3 14567314 1.49E-08 NA
vg1120557960 sf1120091886 11 20557960 8.23E-08 NA
vg0202051269 sf0202051269 2 2051269 8.79E-08 NA
vg1120940295 sf1120474198 11 20940295 9.42E-08 2.56E-06
vg1120560286 sf1120094212 11 20560286 2.43E-07 NA
vg0407630134 sf0407625401 4 7630134 3.78E-07 1.91E-06
vg0700893465 sf0700892465 7 893465 2.51E-06 NA