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 mr1467 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
vg0135794714 sf0135793671 1 35794714 1.92E-07 3.17E-07
vg0616167039 sf0616166041 6 16167039 2.28E-07 4.55E-06
vg0104322740 sf0104321740 1 4322740 3.83E-06 4.97E-06
vg0123406476 sf0123405432 1 23406476 NA 1.00E-06
vg0717154554 sf0717153561 7 17154554 NA 4.41E-06