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 mr1682 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
vg0727185062 sf0727184068 7 27185062 1.18E-23 NA
vg0307039146 sf0307038144 3 7039146 1.12E-22 NA
vg0129349785 sf0129348740 1 29349785 8.27E-22 NA
vg0823030389 sf0823027676 8 23030389 2.66E-21 NA
vg0204918488 sf0204918485 2 4918488 5.57E-21 3.27E-06
vg1009605363 sf1009534184 10 9605363 1.49E-17 NA
vg0142427760 sf0142426716 1 42427760 NA 1.43E-06
vg0717352217 sf0717351224 7 17352217 NA 2.38E-06
vg0709235829 sf0709234835 7 9235829 NA 6.46E-06