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 mr1702 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
vg0119495785 sf0119494740 1 19495785 1.89E-08 5.84E-06
vg0726930454 sf0726929460 7 26930454 2.34E-08 NA
vg0119926212 sf0119925167 1 19926212 2.49E-08 1.76E-06
vg0431411704 sf0431226602 4 31411704 1.19E-07 1.98E-06
vg0918843192 sf0918842192 9 18843192 NA 1.57E-06