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 mr1738 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
vg0805946030 sf0805945033 8 5946030 3.52E-12 4.39E-08
vg0124420479 sf0124419435 1 24420479 1.37E-09 4.99E-06
vg0222002131 sf0221996262 2 22002131 2.38E-09 5.50E-08
vg1211898266 sf1211895601 12 11898266 3.54E-08 1.92E-06
vg1001247868 sf1001246845 10 1247868 5.15E-08 2.99E-06
vg0500776377 sf0500776359 5 776377 9.36E-08 4.64E-06
vg0317372993 sf0317371803 3 17372993 9.38E-08 1.54E-06
vg0606109335 sf0606108336 6 6109335 3.18E-06 1.75E-06