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 mr1559 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
vg0216691537 sf0216685667 2 16691537 5.33E-12 6.95E-08
vg0216625467 sf0216619597 2 16625467 1.08E-11 4.21E-08
vg0216660781 sf0216654911 2 16660781 4.32E-11 3.30E-08
vg1005364262 sf1005380799 10 5364262 5.51E-08 NA
vg1127682350 sf1127210737 11 27682350 6.68E-08 NA
vg0216301746 sf0216295876 2 16301746 7.74E-08 NA
vg0335000939 sf0334993809 3 35000939 1.51E-07 3.49E-07
vg1219945538 sf1219917008 12 19945538 4.83E-07 1.17E-06
vg0201945422 sf0201945422 2 1945422 2.08E-06 2.94E-06
vg0824571069 sf0824568355 8 24571069 3.10E-06 1.42E-06
vg0208159232 sf0208159231 2 8159232 NA 2.71E-07