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 mr1799 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
vg0205810722 sf0205810722 2 5810722 2.76E-06 2.76E-06
vg0431655631 sf0431470524 4 31655631 2.86E-06 2.86E-06
vg0725535785 sf0725534791 7 25535785 3.28E-06 3.28E-06
vg0414114398 sf0414105113 4 14114398 4.95E-06 4.95E-06
vg0138861491 sf0138860448 1 38861491 5.35E-06 5.35E-06