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 mr1258 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
vg1013651895 sf1013580664 10 13651895 1.59E-16 NA
vg0223629300 sf0223623431 2 23629300 3.67E-15 NA
vg0207019221 sf0207019221 2 7019221 5.73E-15 NA
vg0727066911 sf0727065917 7 27066911 1.09E-14 NA
vg0232180481 sf0232174612 2 32180481 1.10E-14 NA
vg1006265706 sf1006281329 10 6265706 4.97E-13 3.31E-13
vg0921852094 sf0921851613 9 21852094 1.14E-12 NA
vg1009165299 sf1009094120 10 9165299 3.91E-12 4.11E-11
vg1007469091 sf1007484714 10 7469091 4.30E-12 6.43E-07
vg0407822256 sf0407817524 4 7822256 7.40E-12 1.97E-08
vg1006529910 sf1006545533 10 6529910 NA 6.56E-09
vg1216843191 sf1216837145 12 16843191 NA 4.78E-08
vg1204314449 sf1204313437 12 4314449 NA 1.17E-07
vg1009720372 sf1009649193 10 9720372 NA 1.48E-07
vg1010531505 sf1010460326 10 10531505 NA 3.08E-07
vg0528415027 sf0528352382 5 28415027 NA 4.75E-07
vg0716828374 sf0716827381 7 16828374 NA 5.19E-07
vg1006277551 sf1006293174 10 6277551 NA 7.75E-07
vg0403205910 sf0403201513 4 3205910 NA 3.12E-06
vg1009946077 sf1009874898 10 9946077 NA 4.67E-06