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 mr1401 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
vg1213936261 sf1213933599 12 13936261 3.48E-09 NA
vg1216469080 sf1216466373 12 16469080 6.43E-09 NA
vg0808633073 sf0808632077 8 8633073 7.01E-09 2.31E-06
vg0311016054 sf0311014772 3 11016054 1.00E-08 NA
vg0502333732 sf0502333707 5 2333732 1.21E-08 NA
vg1006612280 sf1006627903 10 6612280 3.14E-06 3.66E-06