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 mr1699 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
vg0107080292 sf0107079292 1 7080292 1.54E-26 5.53E-08
vg0233314549 sf0233308680 2 33314549 9.38E-23 NA
vg0212210356 sf0212210352 2 12210356 5.51E-22 NA
vg0609313418 sf0609312419 6 9313418 9.06E-22 NA
vg0414156862 sf0414147577 4 14156862 2.33E-21 NA
vg0724490482 sf0724489488 7 24490482 NA 1.63E-09