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 mr1318 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
vg0906682620 sf0906681620 9 6682620 9.50E-10 2.97E-06
vg0906637914 sf0906636914 9 6637914 2.34E-09 2.76E-06
vg1214703763 sf1214701104 12 14703763 3.38E-08 NA
vg1215829261 sf1215826558 12 15829261 3.68E-08 NA
vg0429090551 sf0428905407 4 29090551 6.34E-08 NA
vg0223170170 sf0223164301 2 23170170 8.62E-08 NA