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 mr1513 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
vg0224822504 sf0224816635 2 24822504 1.71E-07 2.93E-06
vg0123436071 sf0123435027 1 23436071 1.82E-07 8.42E-07
vg0200658076 sf0200658076 2 658076 4.04E-07 3.04E-06
vg0224592034 sf0224586165 2 24592034 1.58E-06 2.89E-06
vg1217551932 sf1217545887 12 17551932 NA 1.38E-06
vg1207248243 sf1207245650 12 7248243 NA 4.41E-06