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 mr1105 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
vg0525620556 sf0525557977 5 25620556 2.63E-07 2.63E-07
vg0525136576 sf0525073997 5 25136576 8.95E-07 8.94E-07
vg0707853841 sf0707852846 7 7853841 1.23E-06 1.23E-06
vg0205839116 sf0205839116 2 5839116 3.78E-06 3.78E-06
vg1220172445 sf1220143887 12 20172445 3.79E-06 3.79E-06
vg0614725085 sf0614724086 6 14725085 4.28E-06 4.28E-06
vg0715506970 sf0715505977 7 15506970 8.71E-06 8.71E-06