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 mr1570 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
vg0609117647 sf0609116648 6 9117647 2.33E-18 3.22E-10
vg0609205986 sf0609204987 6 9205986 5.56E-17 1.87E-10
vg1011368518 sf1011297337 10 11368518 3.27E-11 NA
vg1020038760 sf1019967258 10 20038760 9.36E-11 NA
vg0823911503 sf0823908789 8 23911503 1.37E-10 NA
vg0231777199 sf0231771330 2 31777199 1.55E-10 NA