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 mr1540 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
vg1125222805 sf1124756645 11 25222805 4.25E-24 NA
vg0516005213 sf0515947721 5 16005213 2.94E-23 NA
vg1216413002 sf1216410295 12 16413002 3.35E-23 NA
vg0804724763 sf0804723766 8 4724763 1.51E-22 NA
vg0529149157 sf0529086512 5 29149157 4.48E-22 NA
vg1217053914 sf1217047868 12 17053914 1.69E-21 3.46E-07
vg1016195699 sf1016124471 10 16195699 1.11E-19 2.14E-06
vg1208083877 sf1208081283 12 8083877 1.13E-19 3.33E-07
vg0129891018 sf0129889973 1 29891018 NA 1.42E-08
vg0726879296 sf0726878302 7 26879296 NA 3.40E-07
vg1115373505 sf1114909819 11 15373505 NA 9.52E-07
vg1218416620 sf1218388056 12 18416620 NA 1.14E-06
vg1218417268 sf1218388704 12 18417268 NA 2.07E-06
vg0827033027 sf0827030313 8 27033027 NA 3.55E-06
vg0314508666 sf0314507354 3 14508666 NA 4.03E-06
vg0918838703 sf0918837703 9 18838703 NA 4.15E-06
vg1209270438 sf1209267848 12 9270438 NA 4.90E-06