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 mr1470 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
vg0626092374 sf0626091377 6 26092374 2.01E-07 2.80E-06
vg0226753616 sf0226747747 2 26753616 2.37E-07 3.29E-06
vg0306212740 sf0306211740 3 6212740 3.86E-07 3.33E-06
vg0529437664 sf0529375019 5 29437664 3.33E-06 NA
vg0314672341 sf0314671028 3 14672341 7.83E-06 NA