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 mr1690 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
vg0122690936 sf0122689891 1 22690936 6.93E-11 1.40E-06
vg0818736737 sf0818734024 8 18736737 3.69E-10 6.96E-06
vg0129279095 sf0129278050 1 29279095 7.01E-10 8.33E-06
vg0233741277 sf0233735408 2 33741277 8.08E-10 NA
vg1010540526 sf1010469347 10 10540526 2.29E-09 NA
vg1215106306 sf1215103643 12 15106306 4.03E-07 8.20E-06