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 mr1748 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
vg0823006156 sf0823003443 8 23006156 7.60E-12 8.31E-08
vg0703878959 sf0703877960 7 3878959 5.69E-11 8.43E-07
vg0225225682 sf0225219813 2 25225682 1.35E-10 3.52E-06
vg0619101816 sf0619100819 6 19101816 1.91E-10 1.19E-06
vg0315367742 sf0315366389 3 15367742 2.25E-10 NA
vg0524300403 sf0524237822 5 24300403 4.55E-10 1.57E-06
vg0114325124 sf0114324098 1 14325124 1.16E-07 NA
vg0220796044 sf0220790176 2 20796044 1.61E-07 NA
vg0706562041 sf0706561046 7 6562041 2.56E-06 NA
vg0820834591 sf0820831878 8 20834591 NA 1.69E-06