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 mr1566 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
vg0316689752 sf0316688398 3 16689752 NA 1.27E-06
vg0901835907 sf0901834907 9 1835907 NA 2.47E-06
vg0402280802 sf0402276397 4 2280802 NA 3.86E-06
vg0316516166 sf0316514811 3 16516166 NA 4.72E-06
vg0816276034 sf0816273320 8 16276034 NA 4.78E-06