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 mr1217 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
vg1224334241 sf1224300694 12 24334241 1.91E-10 9.33E-06
vg0320989254 sf0320987764 3 20989254 1.95E-10 1.06E-07
vg0225541312 sf0225535443 2 25541312 2.53E-10 1.36E-06
vg0318185360 sf0318184142 3 18185360 4.05E-10 NA
vg0802601304 sf0802600307 8 2601304 4.83E-10 NA
vg1216843085 sf1216837039 12 16843085 9.29E-09 4.81E-06