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 mr1643 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
vg0623833223 sf0623832226 6 23833223 4.83E-09 4.83E-09
vg0406853946 sf0406849391 4 6853946 2.43E-07 2.43E-07
vg0132161653 sf0132160609 1 32161653 2.03E-06 2.03E-06
vg0715227955 sf0715226962 7 15227955 2.33E-06 2.33E-06
vg0715817404 sf0715816411 7 15817404 3.78E-06 3.78E-06