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 mr1474 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
vg0712648528 sf0712647535 7 12648528 3.69E-07 3.69E-07
vg0715817404 sf0715816411 7 15817404 7.31E-07 7.31E-07
vg0729692653 sf0729691661 7 29692653 2.26E-06 2.26E-06
vg0406861879 sf0406857324 4 6861879 2.48E-06 2.48E-06
vg0501390670 sf0501390654 5 1390670 3.16E-06 3.16E-06
vg1216898802 sf1216892756 12 16898802 3.20E-06 3.20E-06