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 mr1408 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
vg0611562185 sf0611561186 6 11562185 1.18E-08 9.08E-06
vg0612612601 sf0612611602 6 12612601 2.45E-08 NA
vg0524701771 sf0524639191 5 24701771 2.73E-08 NA
vg1119299829 sf1118833517 11 19299829 2.81E-08 NA
vg0708765167 sf0708764172 7 8765167 3.27E-08 NA
vg0707583684 sf0707582689 7 7583684 3.57E-08 NA
vg1119404611 sf1118938299 11 19404611 6.93E-08 NA
vg0820974361 sf0820971648 8 20974361 NA 3.27E-06