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 mr1608 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
vg0216982985 sf0216977115 2 16982985 5.50E-08 5.50E-08
vg0217098802 sf0217092932 2 17098802 1.00E-07 1.00E-07
vg1221644281 sf1221610828 12 21644281 2.56E-07 2.56E-07
vg0517949741 sf0517889227 5 17949741 3.93E-07 3.93E-07
vg0805565693 sf0805564696 8 5565693 5.97E-07 5.97E-07
vg0619650681 sf0619649684 6 19650681 4.38E-06 4.38E-06
vg1219848125 sf1219819595 12 19848125 4.89E-06 4.89E-06