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 mr1058 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
vg1214822308 sf1214819649 12 14822308 4.79E-07 3.06E-06
vg0130351635 sf0130350591 1 30351635 1.62E-06 2.23E-06
vg0220407461 sf0220401593 2 20407461 2.92E-06 NA
vg1118024765 sf1117558623 11 18024765 4.49E-06 4.53E-06
vg0300249514 sf0300248514 3 249514 4.70E-06 9.48E-06
vg1124078257 sf1123612127 11 24078257 8.82E-06 4.82E-06