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 mr1891 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
vg0139299500 sf0139298457 1 39299500 1.84E-07 1.84E-07
vg0216897057 sf0216891187 2 16897057 4.37E-07 4.37E-07
vg0228272941 sf0228267072 2 28272941 6.56E-07 6.57E-07
vg0225250931 sf0225245062 2 25250931 1.78E-06 1.78E-06
vg0324236046 sf0324234125 3 24236046 2.33E-06 2.33E-06
vg0104429723 sf0104428723 1 4429723 2.94E-06 2.94E-06
vg0114881487 sf0114880461 1 14881487 3.09E-06 3.09E-06
vg0500663064 sf0500663064 5 663064 3.44E-06 3.44E-06
vg0630442371 sf0630441373 6 30442371 3.60E-06 3.60E-06
vg0819491677 sf0819488964 8 19491677 3.67E-06 3.68E-06
vg0704068888 sf0704067889 7 4068888 4.09E-06 4.09E-06
vg0912105771 sf0912104770 9 12105771 4.48E-06 4.48E-06
vg0819113553 sf0819110840 8 19113553 4.51E-06 4.51E-06