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 mr1640 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
vg1117535965 sf1117069820 11 17535965 9.51E-07 9.51E-07
vg0328103960 sf0328097014 3 28103960 1.11E-06 1.11E-06
vg0706605860 sf0706604865 7 6605860 2.90E-06 2.90E-06
vg0910768444 sf0910767443 9 10768444 3.06E-06 3.06E-06
vg1117584893 sf1117118750 11 17584893 3.85E-06 3.85E-06
vg1107947407 sf1107943152 11 7947407 4.63E-06 4.63E-06