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 mr1923 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
vg0115947503 sf0115946477 1 15947503 6.84E-07 8.93E-07
vg0727278538 sf0727277544 7 27278538 2.01E-06 4.98E-06
vg0630108578 sf0630107580 6 30108578 2.41E-06 2.23E-06
vg0331273085 sf0331265970 3 31273085 3.49E-06 6.65E-07
vg1104596397 sf1104592299 11 4596397 3.95E-06 6.58E-07
vg1124114500 sf1123648370 11 24114500 7.01E-06 3.64E-06