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 mr1382 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
vg0200463356 sf0200463356 2 463356 2.60E-07 2.60E-07
vg0226817183 sf0226811314 2 26817183 3.18E-07 3.18E-07
vg0432523363 sf0432338255 4 32523363 3.25E-07 3.25E-07
vg0500825126 sf0500825108 5 825126 7.73E-07 7.73E-07
vg0819439794 sf0819437081 8 19439794 1.36E-06 1.36E-06
vg0507114582 sf0507114524 5 7114582 2.72E-06 2.72E-06
vg0330235385 sf0330228424 3 30235385 4.69E-06 4.69E-06