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 mr1144 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
vg0610609054 sf0610608055 6 10609054 2.39E-10 2.39E-10
vg0610760933 sf0610759934 6 10760933 2.30E-08 2.30E-08
vg0616129303 sf0616128305 6 16129303 7.47E-08 7.47E-08
vg1220360637 sf1220332079 12 20360637 2.76E-07 2.76E-07
vg0913099185 sf0913098184 9 13099185 2.89E-07 2.89E-07
vg1105967574 sf1105963326 11 5967574 6.87E-07 6.87E-07
vg1208009403 sf1208006809 12 8009403 1.33E-06 1.33E-06
vg1004372036 sf1004388574 10 4372036 1.48E-06 1.48E-06
vg0611526397 sf0611525398 6 11526397 2.28E-06 2.28E-06
vg0409654224 sf0409644922 4 9654224 3.55E-06 3.55E-06
vg0701479081 sf0701478081 7 1479081 4.46E-06 4.46E-06