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 mr1686 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
vg1111313699 sf1111308016 11 11313699 1.27E-06 1.22E-06
vg0434823384 sf0434638275 4 34823384 2.97E-06 3.85E-06
vg0225417219 sf0225411350 2 25417219 3.93E-06 4.63E-06
vg0407698181 sf0407693448 4 7698181 4.15E-06 2.85E-06
vg0424988272 sf0424803133 4 24988272 4.31E-06 2.42E-06
vg0328066679 sf0328059733 3 28066679 8.18E-06 4.41E-06