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 mr1257 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
vg0216763637 sf0216757767 2 16763637 4.23E-15 3.02E-10
vg0506159272 sf0506159211 5 6159272 4.42E-11 NA
vg1216454490 sf1216451783 12 16454490 1.03E-10 NA
vg1125139237 sf1124673077 11 25139237 9.23E-10 NA
vg0425552229 sf0425367089 4 25552229 1.51E-09 NA
vg1011966171 sf1011894986 10 11966171 NA 5.31E-06