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 mr1830 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
vg0410901198 sf0410891899 4 10901198 6.06E-11 4.60E-06
vg0408360478 sf0408355752 4 8360478 8.77E-11 4.47E-06
vg0412540776 sf0412531486 4 12540776 2.92E-10 3.31E-06
vg0409475911 sf0409466609 4 9475911 4.22E-10 1.01E-06
vg0714480578 sf0714479585 7 14480578 2.63E-09 NA
vg0518411174 sf0518350660 5 18411174 6.12E-09 NA
vg0519052323 sf0518989807 5 19052323 8.08E-09 NA
vg0723125324 sf0723124331 7 23125324 1.50E-08 4.55E-06
vg0518410596 sf0518350082 5 18410596 1.65E-08 NA
vg0321991817 sf0321990324 3 21991817 6.30E-06 6.01E-06
vg0500210720 sf0500210720 5 210720 8.53E-06 NA