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 mr1916 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
vg0106921094 sf0106920094 1 6921094 2.07E-25 7.26E-11
vg0106836437 sf0106835437 1 6836437 9.11E-25 4.53E-11
vg0430737908 sf0430552781 4 30737908 4.44E-20 NA
vg0612902025 sf0612901026 6 12902025 1.39E-19 NA
vg0106675625 sf0106674625 1 6675625 3.01E-19 1.52E-13
vg0628086657 sf0628085659 6 28086657 6.98E-19 NA
vg0801623800 sf0801622802 8 1623800 2.76E-17 2.80E-06
vg0106679257 sf0106678257 1 6679257 7.40E-17 2.69E-14
vg0712115251 sf0712114257 7 12115251 1.01E-16 NA
vg0112054957 sf0112053931 1 12054957 4.05E-15 NA
vg0102692289 sf0102691289 1 2692289 NA 1.16E-07
vg0224035929 sf0224030060 2 24035929 NA 1.26E-07
vg0313128846 sf0313127564 3 13128846 NA 1.43E-07
vg0911638105 sf0911637104 9 11638105 NA 7.82E-07
vg0106675319 sf0106674319 1 6675319 NA 9.82E-07
vg0106987726 sf0106986726 1 6987726 NA 1.26E-06
vg0105078015 sf0105077015 1 5078015 NA 3.53E-06