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 mr1760 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
vg1121898365 sf1121432236 11 21898365 3.27E-08 3.28E-08
vg0804905723 sf0804904726 8 4905723 8.75E-08 8.75E-08
vg0317372993 sf0317371803 3 17372993 5.41E-07 5.41E-07
vg0805946030 sf0805945033 8 5946030 1.32E-06 1.32E-06
vg0219761806 sf0219755938 2 19761806 2.95E-06 2.95E-06
vg0321576069 sf0321574579 3 21576069 3.27E-06 3.27E-06
vg0904629329 sf0904628329 9 4629329 4.17E-06 4.17E-06
vg0227859855 sf0227853986 2 27859855 4.85E-06 4.85E-06
vg0606311325 sf0606310326 6 6311325 4.86E-06 4.86E-06