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 mr1672 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
vg0400407869 sf0400406867 4 407869 7.81E-13 9.24E-12
vg0138126205 sf0138125162 1 38126205 7.75E-10 1.80E-07
vg0137919286 sf0137918243 1 37919286 3.15E-09 3.03E-07
vg0811517885 sf0811516890 8 11517885 5.51E-08 NA
vg0400397491 sf0400396489 4 397491 NA 2.16E-06