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 mr1296 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
vg0217523635 sf0217517765 2 17523635 7.02E-07 7.02E-07
vg0622302745 sf0622301748 6 22302745 1.25E-06 1.25E-06
vg1210109920 sf1210107331 12 10109920 1.80E-06 1.80E-06
vg0608039241 sf0608038242 6 8039241 1.86E-06 1.86E-06
vg0804040328 sf0804039331 8 4040328 2.55E-06 2.55E-06
vg1215207910 sf1215205208 12 15207910 3.35E-06 3.35E-06
vg0608037462 sf0608036463 6 8037462 4.61E-06 4.61E-06