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 mr1198 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
vg0216971299 sf0216965429 2 16971299 2.42E-13 3.33E-07
vg0820974361 sf0820971648 8 20974361 3.89E-12 NA
vg1207382540 sf1207379947 12 7382540 8.38E-12 NA
vg0220869217 sf0220863349 2 20869217 1.47E-11 NA
vg0710418364 sf0710417370 7 10418364 1.71E-11 NA
vg1215169176 sf1215166512 12 15169176 NA 2.40E-06
vg0315932136 sf0315930783 3 15932136 NA 3.57E-06
vg0726174758 sf0726173764 7 26174758 NA 4.17E-06