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 mr1521 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
vg0419220060 sf0419048098 4 19220060 9.94E-21 3.09E-10
vg0419219689 sf0419047727 4 19219689 1.13E-20 2.72E-10
vg1219408131 sf1219379601 12 19408131 9.89E-18 NA
vg0810613276 sf0810612280 8 10613276 1.43E-17 NA
vg0419889132 sf0419717168 4 19889132 2.49E-17 NA
vg0814311518 sf0814308804 8 14311518 1.15E-16 NA
vg0418804144 sf0418632189 4 18804144 5.20E-15 1.08E-06
vg0417328671 sf0417156713 4 17328671 NA 5.76E-06