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 mr1346 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
vg0500853907 sf0500853889 5 853907 2.48E-08 4.69E-06
vg1214644504 sf1214641844 12 14644504 5.21E-08 4.63E-06
vg0400771041 sf0400770041 4 771041 1.39E-06 NA
vg0123593589 sf0123592545 1 23593589 4.51E-06 4.33E-06
vg0407728955 sf0407724222 4 7728955 4.73E-06 NA
vg1206203799 sf1206202689 12 6203799 6.36E-06 NA
vg0233859530 sf0233853661 2 33859530 NA 5.40E-06