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 mr1649 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
vg0217018976 sf0217013106 2 17018976 9.76E-09 9.03E-06
vg0826158875 sf0826156161 8 26158875 1.17E-08 4.21E-08
vg0406994122 sf0406989393 4 6994122 2.41E-08 5.67E-06
vg0216616673 sf0216610803 2 16616673 7.47E-08 9.16E-07
vg0216615616 sf0216609746 2 16615616 7.48E-08 3.71E-07