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 mr1517 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
vg0137881242 sf0137880199 1 37881242 7.30E-122 1.77E-21
vg0133455832 sf0133454788 1 33455832 5.67E-97 NA
vg0214383856 sf0214377986 2 14383856 1.30E-96 NA
vg0717047704 sf0717046711 7 17047704 4.17E-96 1.56E-06
vg0134540544 sf0134539501 1 34540544 2.08E-95 1.14E-06
vg1114733114 sf1114269428 11 14733114 3.97E-92 NA
vg0137820754 sf0137819711 1 37820754 7.74E-90 3.89E-22
vg0714554251 sf0714553258 7 14554251 4.18E-85 4.92E-06
vg0137885756 sf0137884713 1 37885756 NA 1.68E-10
vg0717362404 sf0717361411 7 17362404 NA 7.31E-10
vg0124267851 sf0124266807 1 24267851 NA 1.87E-07
vg0711095110 sf0711094116 7 11095110 NA 2.27E-07
vg1121911743 sf1121445614 11 21911743 NA 4.77E-07
vg0311534838 sf0311533556 3 11534838 NA 1.65E-06
vg0135141098 sf0135140055 1 35141098 NA 1.88E-06
vg0124206667 sf0124205623 1 24206667 NA 2.31E-06
vg0614107939 sf0614106940 6 14107939 NA 2.76E-06