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 mr1828 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
vg0206383144 sf0206383144 2 6383144 8.35E-43 NA
vg0616967907 sf0616966910 6 16967907 4.78E-41 NA
vg0823014174 sf0823011461 8 23014174 8.44E-41 NA
vg0526234170 sf0526171534 5 26234170 1.19E-40 9.67E-06
vg0628529241 sf0628528243 6 28529241 2.63E-40 NA
vg0523265069 sf0523202490 5 23265069 1.44E-39 1.31E-06
vg0807128963 sf0807127968 8 7128963 1.11E-38 2.84E-06
vg0710366378 sf0710365384 7 10366378 4.99E-37 2.72E-06
vg0526174493 sf0526111913 5 26174493 1.05E-36 3.95E-06
vg0605814911 sf0605813912 6 5814911 NA 1.37E-06
vg1004737301 sf1004753838 10 4737301 NA 4.72E-06