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 mr1209 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
vg1124303443 sf1123837313 11 24303443 2.70E-07 1.26E-06
vg1219850678 sf1219822148 12 19850678 4.62E-07 1.80E-06
vg1222419938 sf1222386377 12 22419938 5.17E-07 2.72E-06
vg1207456492 sf1207453898 12 7456492 9.53E-07 4.25E-06
vg1220271826 sf1220243268 12 20271826 1.04E-06 3.78E-06
vg1214656787 sf1214654127 12 14656787 5.74E-06 NA