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 mr1643 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 5.71E-07 5.72E-07
vg0628359678 sf0628358680 6 28359678 6.18E-07 6.19E-07
vg0431515534 sf0431330433 4 31515534 1.75E-06 1.75E-06
vg0607338126 sf0607337127 6 7338126 3.24E-06 3.24E-06
vg0908960274 sf0908959273 9 8960274 4.90E-06 4.92E-06