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 mr1780 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
vg1215969771 sf1215967067 12 15969771 1.60E-09 6.65E-08
vg1022582083 sf1022510557 10 22582083 1.68E-08 2.40E-06
vg0912631853 sf0912630852 9 12631853 2.39E-08 NA
vg0208187191 sf0208187190 2 8187191 7.45E-08 NA
vg0912300484 sf0912299483 9 12300484 1.16E-07 6.13E-06
vg1210520286 sf1210517699 12 10520286 1.86E-07 1.78E-07
vg1022580961 sf1022509435 10 22580961 2.00E-07 1.27E-06
vg0715472268 sf0715471275 7 15472268 5.60E-07 2.51E-06
vg1125439473 sf1124973312 11 25439473 6.70E-07 1.47E-06
vg0430745099 sf0430559971 4 30745099 1.73E-06 NA