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 mr1461 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
vg1218169084 sf1218140520 12 18169084 1.87E-08 NA
vg0221533352 sf0221527483 2 21533352 7.36E-08 NA
vg1200182975 sf1200181975 12 182975 1.62E-07 3.69E-06
vg1218237165 sf1218208601 12 18237165 1.47E-06 NA
vg1001246161 sf1001245138 10 1246161 NA 2.96E-06