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 mr1668 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
vg0402803488 sf0402764796 4 2803488 1.27E-08 NA
vg0428446197 sf0428261050 4 28446197 2.25E-08 NA
vg1200274541 sf1200273541 12 274541 4.33E-08 9.15E-06
vg0431615803 sf0431430698 4 31615803 4.61E-08 NA
vg0810250539 sf0810249543 8 10250539 4.96E-08 NA
vg1214823650 sf1214820991 12 14823650 2.88E-06 6.45E-08
vg0411210100 sf0411200801 4 11210100 7.69E-06 NA
vg1012595235 sf1012524050 10 12595235 NA 1.86E-07
vg0223248427 sf0223242558 2 23248427 NA 3.54E-07
vg0608860841 sf0608859842 6 8860841 NA 3.70E-06