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 mr1506 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
vg1218087170 sf1218058606 12 18087170 5.27E-12 2.48E-06
vg0302287012 sf0302286008 3 2287012 1.22E-11 1.14E-06
vg0920288743 sf0920288262 9 20288743 1.52E-11 NA
vg1119446549 sf1118980237 11 19446549 6.22E-11 6.55E-06
vg1119463807 sf1118997495 11 19463807 1.26E-10 1.59E-06
vg1002090827 sf1002089804 10 2090827 2.42E-10 NA