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 mr1499 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
vg0108533994 sf0108532994 1 8533994 1.88E-07 1.88E-07
vg1214642471 sf1214639811 12 14642471 1.89E-07 1.89E-07
vg0135233075 sf0135232032 1 35233075 2.23E-07 2.23E-07
vg0116559161 sf0116558135 1 16559161 1.13E-06 1.13E-06
vg0805792783 sf0805791786 8 5792783 1.26E-06 1.26E-06
vg1211597303 sf1211594639 12 11597303 1.72E-06 1.72E-06
vg0818712613 sf0818709900 8 18712613 2.11E-06 2.11E-06