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 mr1550 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
vg1117484883 sf1117018738 11 17484883 1.51E-09 NA
vg1118719400 sf1118253208 11 18719400 6.72E-09 8.20E-07
vg1116101996 sf1115636868 11 16101996 1.90E-08 4.33E-06
vg0216308622 sf0216302752 2 16308622 7.87E-08 NA
vg1117083295 sf1116617147 11 17083295 8.36E-08 4.26E-06
vg0622932804 sf0622931807 6 22932804 1.47E-07 1.03E-06
vg0820097431 sf0820094718 8 20097431 4.79E-07 3.19E-06
vg1000028876 sf1000027876 10 28876 4.37E-06 1.13E-06