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 mr1569 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
vg1219570780 sf1219542250 12 19570780 1.04E-06 1.05E-06
vg0417918664 sf0417746705 4 17918664 1.30E-06 1.31E-06
vg1214649117 sf1214646457 12 14649117 1.75E-06 1.76E-06
vg1214199203 sf1214196543 12 14199203 1.86E-06 1.87E-06
vg1214600105 sf1214597445 12 14600105 1.91E-06 1.92E-06
vg0130122521 sf0130121476 1 30122521 2.33E-06 2.33E-06