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 mr1306 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
vg0131417081 sf0131416037 1 31417081 3.83E-09 2.69E-06
vg0125906058 sf0125905014 1 25906058 9.66E-07 NA
vg1214600105 sf1214597445 12 14600105 2.16E-06 2.45E-06
vg0317321849 sf0317320659 3 17321849 NA 7.69E-07
vg1215090096 sf1215087437 12 15090096 NA 2.37E-06
vg1125281578 sf1124815418 11 25281578 NA 3.25E-06
vg1125279042 sf1124812882 11 25279042 NA 3.97E-06