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 mr1237 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
vg1122427075 sf1121960946 11 22427075 3.44E-10 3.44E-10
vg0711196263 sf0711195269 7 11196263 2.94E-07 2.94E-07
vg0613038695 sf0613037696 6 13038695 3.76E-07 3.76E-07
vg0713645873 sf0713644880 7 13645873 6.85E-07 6.85E-07
vg0807622017 sf0807621022 8 7622017 8.06E-07 8.06E-07
vg0711201792 sf0711200798 7 11201792 1.00E-06 1.00E-06
vg0715867391 sf0715866398 7 15867391 1.32E-06 1.32E-06
vg0311072594 sf0311071312 3 11072594 1.44E-06 1.44E-06
vg0819969492 sf0819966779 8 19969492 2.14E-06 2.14E-06
vg1004415668 sf1004432206 10 4415668 3.88E-06 3.88E-06
vg0616129303 sf0616128305 6 16129303 4.38E-06 4.38E-06