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 mr1873 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
vg1215482015 sf1215479312 12 15482015 2.10E-09 1.13E-06
vg1214785844 sf1214783185 12 14785844 2.50E-09 9.97E-07
vg0314789758 sf0314788445 3 14789758 4.33E-08 NA
vg0805970126 sf0805969129 8 5970126 5.31E-08 NA
vg0432860646 sf0432675533 4 32860646 NA 4.21E-06