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 mr1100 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
vg0406393570 sf0406389010 4 6393570 3.06E-110 4.07E-20
vg0406561841 sf0406557284 4 6561841 9.39E-108 7.91E-21
vg0122842459 sf0122841415 1 22842459 2.42E-87 NA
vg0612805324 sf0612804325 6 12805324 6.41E-87 2.59E-06
vg0408992109 sf0408987385 4 8992109 1.31E-86 NA
vg1017228554 sf1017157327 10 17228554 1.40E-86 NA
vg0617165924 sf0617164927 6 17165924 5.03E-82 3.93E-06
vg0916689948 sf0916688947 9 16689948 3.07E-81 3.96E-06
vg0613034067 sf0613033068 6 13034067 2.51E-80 2.69E-07
vg0711049866 sf0711048872 7 11049866 1.09E-76 4.05E-06
vg0406521772 sf0406517215 4 6521772 NA 7.13E-09
vg0222745337 sf0222739468 2 22745337 NA 1.91E-08
vg0222742146 sf0222736277 2 22742146 NA 2.23E-08
vg1122466711 sf1122000582 11 22466711 NA 9.55E-08
vg1209905874 sf1209903284 12 9905874 NA 9.69E-08
vg0123735612 sf0123734568 1 23735612 NA 4.18E-07
vg0714594893 sf0714593900 7 14594893 NA 9.77E-07
vg0806593377 sf0806592382 8 6593377 NA 1.16E-06
vg1012696203 sf1012625018 10 12696203 NA 1.48E-06
vg0619710623 sf0619709626 6 19710623 NA 2.70E-06
vg1020493966 sf1020422445 10 20493966 NA 3.64E-06
vg1218763524 sf1218734959 12 18763524 NA 4.15E-06
vg0524201254 sf0524138673 5 24201254 NA 4.60E-06
vg0228609636 sf0228603767 2 28609636 NA 4.88E-06
vg0412008170 sf0411998882 4 12008170 NA 4.98E-06