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 mr1927 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
vg0216929727 sf0216923857 2 16929727 7.18E-11 7.18E-11
vg0216988231 sf0216982361 2 16988231 1.07E-10 1.07E-10
vg0210369537 sf0210369535 2 10369537 1.37E-07 1.37E-07
vg0316411183 sf0316409828 3 16411183 7.73E-07 7.73E-07
vg0507443101 sf0507443043 5 7443101 9.49E-07 9.49E-07
vg0413276176 sf0413266886 4 13276176 2.39E-06 2.39E-06
vg1109425026 sf1109419603 11 9425026 2.46E-06 2.46E-06
vg0803234769 sf0803233772 8 3234769 2.73E-06 2.73E-06
vg0219293036 sf0219287168 2 19293036 3.23E-06 3.23E-06
vg0430949013 sf0430763893 4 30949013 3.29E-06 3.29E-06