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 mr1432 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
vg1118719400 sf1118253208 11 18719400 1.54E-08 3.09E-06
vg1113168608 sf1112704929 11 13168608 2.14E-08 4.22E-06
vg1111043318 sf1111037635 11 11043318 2.99E-08 2.85E-06
vg1122446629 sf1121980500 11 22446629 3.12E-08 1.15E-06
vg1002941120 sf1002940097 10 2941120 8.50E-07 1.76E-06
vg1119374158 sf1118907846 11 19374158 9.57E-07 8.36E-06
vg0411387439 sf0411378142 4 11387439 1.34E-06 9.70E-06
vg0910768444 sf0910767443 9 10768444 2.37E-06 1.24E-06