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
vg1215169176 sf1215166512 12 15169176 5.35E-10 7.55E-08
vg0216971299 sf0216965429 2 16971299 1.51E-07 9.91E-07
vg0714836122 sf0714835129 7 14836122 1.62E-07 4.64E-06
vg1205727635 sf1205726617 12 5727635 2.24E-07 3.60E-06
vg0610865756 sf0610864757 6 10865756 1.33E-06 NA
vg0315931790 sf0315930437 3 15931790 3.32E-06 3.69E-06