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 mr1229 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
vg1011340145 sf1011268965 10 11340145 4.54E-12 8.09E-06
vg0402403687 sf0402399282 4 2403687 5.24E-11 NA
vg0722226606 sf0722225613 7 22226606 1.07E-10 NA
vg0426664369 sf0426479243 4 26664369 1.10E-10 NA
vg0223276067 sf0223270198 2 23276067 2.89E-10 NA
vg1011673523 sf1011602338 10 11673523 3.89E-10 NA