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 mr1756 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
vg0400167321 sf0400166321 4 167321 3.59E-12 1.19E-07
vg0506307569 sf0506307508 5 6307569 9.01E-11 NA
vg0430737863 sf0430552736 4 30737863 1.15E-10 NA
vg0520041619 sf0519979095 5 20041619 1.27E-10 NA
vg0222948971 sf0222943102 2 22948971 2.61E-10 NA
vg1214404531 sf1214401872 12 14404531 6.55E-08 NA