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 mr1217 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
vg1018636841 sf1018565398 10 18636841 1.11E-17 1.56E-06
vg1103861273 sf1103857175 11 3861273 2.92E-16 NA
vg1214674613 sf1214671952 12 14674613 7.10E-16 NA
vg0800238613 sf0800237613 8 238613 7.53E-16 NA
vg1004566535 sf1004583073 10 4566535 8.40E-16 9.72E-06
vg1214674666 sf1214672005 12 14674666 9.94E-16 3.68E-06
vg1214822308 sf1214819649 12 14822308 NA 4.29E-06