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 mr1861 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
vg0222741535 sf0222735666 2 22741535 4.17E-98 3.83E-37
vg0222719698 sf0222713829 2 22719698 6.49E-97 1.45E-38
vg0705305606 sf0705304607 7 5305606 1.51E-56 NA
vg0626793010 sf0626792013 6 26793010 6.58E-56 NA
vg0917380686 sf0917379685 9 17380686 1.16E-54 8.62E-06
vg0501641431 sf0501641415 5 1641431 2.32E-53 NA
vg0222725003 sf0222719134 2 22725003 NA 1.58E-15
vg0222857256 sf0222851387 2 22857256 NA 1.63E-08
vg0223755105 sf0223749236 2 23755105 NA 6.55E-08
vg0222817468 sf0222811599 2 22817468 NA 7.52E-08
vg0224381772 sf0224375903 2 24381772 NA 1.05E-06
vg0421093803 sf0420921855 4 21093803 NA 3.97E-06
vg0516694037 sf0516633679 5 16694037 NA 9.63E-06