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 mr1753 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
vg0141835922 sf0141834879 1 41835922 1.02E-06 1.02E-06
vg0332499847 sf0332492720 3 32499847 1.07E-06 1.07E-06
vg0328919612 sf0328912664 3 28919612 1.37E-06 1.37E-06
vg0328202089 sf0328195143 3 28202089 1.63E-06 1.64E-06
vg0711906132 sf0711905138 7 11906132 3.01E-06 3.01E-06
vg0420654451 sf0420482494 4 20654451 4.43E-06 4.44E-06