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 mr1689 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
vg1013262331 sf1013191101 10 13262331 4.31E-42 NA
vg1017569988 sf1017498761 10 17569988 2.34E-41 NA
vg0826027845 sf0826025131 8 26027845 2.72E-41 NA
vg0522067748 sf0522005190 5 22067748 2.72E-40 NA
vg0921847884 sf0921847403 9 21847884 5.72E-40 NA
vg0528017915 sf0527955271 5 28017915 1.03E-35 NA
vg0918694631 sf0918693630 9 18694631 NA 8.62E-07
vg0518984986 sf0518922470 5 18984986 NA 3.80E-06