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 mr1485 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
vg0212359529 sf0212359525 2 12359529 9.43E-07 9.43E-07
vg0406861879 sf0406857324 4 6861879 1.36E-06 1.36E-06
vg0105159820 sf0105158820 1 5159820 1.69E-06 1.69E-06
vg0604048797 sf0604047798 6 4048797 1.95E-06 1.95E-06
vg0316685104 sf0316683749 3 16685104 2.17E-06 2.17E-06
vg0105172050 sf0105171050 1 5172050 4.86E-06 4.86E-06