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 mr1932 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
vg0235531396 sf0235525527 2 35531396 2.03E-35 NA
vg0106781087 sf0106780087 1 6781087 1.14E-34 NA
vg0332051163 sf0332044040 3 32051163 1.37E-34 NA
vg0529544194 sf0529481549 5 29544194 2.87E-34 NA
vg0134942609 sf0134941566 1 34942609 3.28E-34 NA
vg0610482838 sf0610481839 6 10482838 3.53E-30 5.47E-07
vg0514056661 sf0513999205 5 14056661 NA 1.92E-06