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 mr1048 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
vg0709984451 sf0709983457 7 9984451 6.63E-08 6.63E-08
vg0820974361 sf0820971648 8 20974361 3.87E-07 3.88E-07
vg1210206055 sf1210203466 12 10206055 2.07E-06 2.07E-06
vg0433638267 sf0433453150 4 33638267 2.42E-06 2.42E-06
vg1216422805 sf1216420098 12 16422805 2.46E-06 2.46E-06
vg1105377831 sf1105373582 11 5377831 2.67E-06 2.67E-06
vg1214822308 sf1214819649 12 14822308 2.89E-06 2.89E-06
vg1005659181 sf1005675719 10 5659181 3.12E-06 3.12E-06