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 mr1819 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
vg1217551737 sf1217545692 12 17551737 4.48E-09 2.12E-06
vg0601988659 sf0601987660 6 1988659 1.16E-08 5.84E-07
vg0113687946 sf0113686920 1 13687946 2.56E-08 NA
vg1217863038 sf1217834472 12 17863038 5.96E-08 NA
vg0420557418 sf0420385462 4 20557418 8.58E-08 1.16E-06
vg0818421321 sf0818418608 8 18421321 2.78E-07 1.59E-06
vg0108533994 sf0108532994 1 8533994 3.79E-06 1.45E-06