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 mr1468 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
vg0140997622 sf0140996579 1 40997622 3.24E-07 3.24E-07
vg1200200887 sf1200199887 12 200887 5.74E-07 5.74E-07
vg0828208021 sf0828205307 8 28208021 1.37E-06 1.37E-06
vg0214178657 sf0214172787 2 14178657 1.54E-06 1.54E-06
vg0222019495 sf0222013626 2 22019495 1.63E-06 1.63E-06
vg0406869281 sf0406864726 4 6869281 1.69E-06 1.69E-06
vg1105512758 sf1105508509 11 5512758 3.51E-06 3.51E-06
vg0421433477 sf0421261529 4 21433477 4.80E-06 4.80E-06
vg0711639300 sf0711638306 7 11639300 8.25E-06 8.25E-06