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 mr1458 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
vg1218529611 sf1218501047 12 18529611 7.40E-40 1.59E-20
vg1218514358 sf1218485794 12 18514358 9.58E-35 6.46E-20
vg1218588565 sf1218560001 12 18588565 1.73E-22 2.83E-16
vg1219408917 sf1219380387 12 19408917 1.43E-16 3.71E-08
vg1217551737 sf1217545692 12 17551737 5.25E-16 5.79E-10
vg1218207876 sf1218179312 12 18207876 1.26E-15 1.09E-06
vg1218704534 sf1218675969 12 18704534 1.31E-13 4.87E-13
vg1218832355 sf1218803790 12 18832355 1.99E-13 5.33E-07
vg0406750129 sf0406745575 4 6750129 5.31E-13 4.51E-08
vg1218936276 sf1218907711 12 18936276 5.68E-13 2.52E-08
vg1217338702 sf1217332657 12 17338702 1.07E-12 1.55E-06
vg1218294715 sf1218266151 12 18294715 1.96E-12 5.19E-09
vg1218612392 sf1218583828 12 18612392 1.27E-09 5.98E-08
vg1218153891 sf1218125327 12 18153891 3.07E-08 8.13E-07
vg1216602715 sf1216600008 12 16602715 3.09E-08 7.56E-08
vg0224287184 sf0224281315 2 24287184 5.73E-08 3.64E-06
vg1219400445 sf1219371915 12 19400445 NA 5.68E-08
vg1216898780 sf1216892734 12 16898780 NA 5.38E-07
vg0216594674 sf0216588804 2 16594674 NA 8.48E-07
vg1109865325 sf1109859902 11 9865325 NA 1.83E-06
vg1216968197 sf1216962151 12 16968197 NA 2.36E-06
vg1218294806 sf1218266242 12 18294806 NA 2.45E-06
vg1217370443 sf1217364398 12 17370443 NA 2.71E-06