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 mr1964 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
vg0200660296 sf0200660296 2 660296 2.11E-07 3.32E-06
vg0224822504 sf0224816635 2 24822504 3.78E-07 4.72E-06
vg0224512632 sf0224506763 2 24512632 1.94E-06 4.09E-06
vg1226056282 sf1226022676 12 26056282 5.10E-06 2.22E-06
vg0107333687 sf0107332687 1 7333687 7.53E-06 NA
vg1207257056 sf1207254463 12 7257056 8.25E-06 5.99E-07
vg1207220741 sf1207218137 12 7220741 9.95E-06 8.74E-07
vg1217551932 sf1217545887 12 17551932 NA 2.92E-06
vg0208268939 sf0208268938 2 8268939 NA 6.50E-06