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 mr1228 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
vg1102381224 sf1102377083 11 2381224 4.47E-07 4.48E-07
vg1219159089 sf1219130523 12 19159089 4.71E-07 4.71E-07
vg0603938117 sf0603937118 6 3938117 9.64E-07 9.65E-07
vg0314419391 sf0314418080 3 14419391 2.25E-06 2.25E-06
vg0418084715 sf0417912756 4 18084715 2.51E-06 2.51E-06
vg0225962935 sf0225957066 2 25962935 3.91E-06 3.91E-06