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 mr1736 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
vg0416978994 sf0416807036 4 16978994 1.17E-06 1.17E-06
vg1002234112 sf1002233089 10 2234112 1.52E-06 1.52E-06
vg0407996034 sf0407991303 4 7996034 1.85E-06 1.85E-06
vg0629450401 sf0629449403 6 29450401 2.50E-06 2.50E-06
vg1216760958 sf1216754912 12 16760958 2.52E-06 2.52E-06
vg1226569792 sf1226536187 12 26569792 3.26E-06 3.26E-06
vg0113669388 sf0113668362 1 13669388 3.56E-06 3.56E-06