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 mr1853 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
vg0714435991 sf0714434998 7 14435991 1.25E-07 1.25E-07
vg1207459186 sf1207456592 12 7459186 3.18E-07 3.18E-07
vg1208166494 sf1208163900 12 8166494 5.18E-07 5.18E-07
vg1207383759 sf1207381166 12 7383759 6.68E-07 6.68E-07
vg1214399949 sf1214397290 12 14399949 7.51E-07 7.51E-07
vg1213127911 sf1213125249 12 13127911 7.70E-07 7.70E-07
vg1124078478 sf1123612348 11 24078478 9.44E-07 9.44E-07
vg0213591886 sf0213591882 2 13591886 1.10E-06 1.10E-06
vg1212139228 sf1212136564 12 12139228 1.24E-06 1.24E-06
vg1214943582 sf1214940924 12 14943582 1.25E-06 1.25E-06
vg0608456977 sf0608455978 6 8456977 1.36E-06 1.36E-06
vg1004561271 sf1004577809 10 4561271 2.11E-06 2.11E-06
vg0604130041 sf0604129042 6 4130041 2.53E-06 2.53E-06
vg1209793056 sf1209790466 12 9793056 4.26E-06 4.27E-06