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 mr1058 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
vg1215167085 sf1215164421 12 15167085 7.94E-07 7.97E-07
vg0200528076 sf0200528076 2 528076 1.21E-06 1.21E-06
vg1215266864 sf1215264162 12 15266864 2.04E-06 2.04E-06
vg0115958705 sf0115957679 1 15958705 2.37E-06 2.38E-06
vg1004557426 sf1004573964 10 4557426 4.00E-06 4.02E-06
vg0220407461 sf0220401593 2 20407461 4.90E-06 4.93E-06
vg0706162756 sf0706161757 7 6162756 5.56E-06 5.58E-06
vg0431515534 sf0431330433 4 31515534 5.66E-06 5.67E-06