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 mr1173 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
vg1215401891 sf1215399189 12 15401891 1.81E-07 1.10E-06
vg0911441487 sf0911440486 9 11441487 4.87E-07 8.11E-06
vg1212386844 sf1212384183 12 12386844 7.76E-07 1.11E-06
vg0729037919 sf0729036927 7 29037919 8.08E-07 3.45E-06
vg1216106203 sf1216103499 12 16106203 4.75E-06 3.39E-06
vg0414209097 sf0414199813 4 14209097 NA 6.55E-06