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 mr1293 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
vg0407000775 sf0406996046 4 7000775 7.76E-07 7.76E-07
vg1117584893 sf1117118750 11 17584893 1.25E-06 1.25E-06
vg0314912614 sf0314911261 3 14912614 1.53E-06 1.53E-06
vg0140479964 sf0140478921 1 40479964 2.14E-06 2.14E-06
vg0125127326 sf0125126282 1 25127326 3.97E-06 3.97E-06
vg0200486470 sf0200486470 2 486470 4.12E-06 4.12E-06