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 mr1364 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
vg0720359934 sf0720358941 7 20359934 2.69E-12 NA
vg0720416740 sf0720415747 7 20416740 4.39E-12 NA
vg0729153599 sf0729152607 7 29153599 4.82E-12 NA
vg0706185610 sf0706184611 7 6185610 7.23E-12 NA
vg0529113098 sf0529050453 5 29113098 9.57E-12 NA
vg0108525900 sf0108524900 1 8525900 1.74E-11 NA
vg1215794097 sf1215791394 12 15794097 3.86E-09 2.28E-06