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 mr1681 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
vg0130290451 sf0130289406 1 30290451 5.80E-09 1.47E-07
vg0433595407 sf0433410291 4 33595407 6.31E-08 1.46E-06
vg0529099493 sf0529036848 5 29099493 1.29E-07 2.50E-06
vg0433598971 sf0433413855 4 33598971 1.65E-07 2.00E-06
vg0703264096 sf0703263097 7 3264096 5.59E-07 3.96E-06
vg0300249514 sf0300248514 3 249514 2.01E-06 1.72E-06
vg0502062829 sf0502062811 5 2062829 2.87E-06 7.13E-06
vg0117360571 sf0117359525 1 17360571 6.16E-06 4.69E-06