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 mr1832 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
vg0802222500 sf0802221503 8 2222500 3.62E-07 3.62E-07
vg0328874978 sf0328868031 3 28874978 6.99E-07 6.99E-07
vg0125460306 sf0125459262 1 25460306 8.98E-07 8.98E-07
vg0125127326 sf0125126282 1 25127326 1.20E-06 1.20E-06
vg0132256380 sf0132255336 1 32256380 3.37E-06 3.37E-06
vg1117176992 sf1116710844 11 17176992 4.84E-06 4.85E-06