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 mr1227 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
vg0719208938 sf0719207945 7 19208938 1.17E-10 1.88E-07
vg0913973334 sf0913972333 9 13973334 1.25E-08 2.48E-06
vg0724951834 sf0724950840 7 24951834 5.17E-08 NA
vg0314222238 sf0314220927 3 14222238 7.85E-08 NA
vg0613380876 sf0613379877 6 13380876 2.86E-07 2.86E-06
vg0614844474 sf0614843475 6 14844474 3.48E-07 1.64E-06