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 mr1751 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
vg0709984451 sf0709983457 7 9984451 1.01E-14 4.41E-06
vg0725433712 sf0725432718 7 25433712 7.86E-14 NA
vg1119916329 sf1119450252 11 19916329 1.46E-12 NA
vg0711642430 sf0711641436 7 11642430 2.39E-12 6.78E-06
vg1219760769 sf1219732239 12 19760769 5.29E-12 2.54E-06
vg1105526623 sf1105522374 11 5526623 6.60E-12 NA
vg0518984986 sf0518922470 5 18984986 7.73E-10 1.55E-06
vg1017959818 sf1017888590 10 17959818 NA 1.11E-06
vg1214656787 sf1214654127 12 14656787 NA 1.82E-06