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 mr1282 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
vg0919855604 sf0919855123 9 19855604 2.67E-09 1.64E-06
vg0803653778 sf0803652781 8 3653778 1.23E-08 NA
vg1203660130 sf1203659129 12 3660130 1.77E-08 NA
vg0134272325 sf0134271282 1 34272325 3.53E-08 NA
vg0819275819 sf0819273106 8 19275819 3.65E-08 NA
vg1216757238 sf1216751192 12 16757238 1.25E-06 NA
vg0619103677 sf0619102680 6 19103677 3.95E-06 1.34E-06