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 mr1865 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
vg0723509971 sf0723508978 7 23509971 5.08E-10 3.95E-06
vg1208506304 sf1208503711 12 8506304 9.75E-10 NA
vg0800629037 sf0800628037 8 629037 2.26E-09 NA
vg0419531874 sf0419359912 4 19531874 4.37E-09 NA
vg0231913229 sf0231907360 2 31913229 1.78E-08 3.91E-06
vg0709622923 sf0709621929 7 9622923 3.15E-08 3.24E-06
vg0231672631 sf0231666762 2 31672631 1.68E-07 NA
vg0406655358 sf0406650802 4 6655358 5.79E-07 2.67E-06
vg0620778091 sf0620777094 6 20778091 8.24E-07 1.77E-06
vg0601150840 sf0601149841 6 1150840 1.01E-06 3.95E-06
vg0502245051 sf0502245026 5 2245051 1.96E-06 3.45E-06
vg0506844240 sf0506844182 5 6844240 3.90E-06 2.76E-06
vg1119005779 sf1118539467 11 19005779 4.42E-06 1.79E-06
vg0502297050 sf0502297025 5 2297050 5.70E-06 3.74E-06
vg0415909654 sf0415737687 4 15909654 8.30E-06 NA