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 mr1769 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
vg0106691928 sf0106690928 1 6691928 1.06E-52 9.77E-28
vg0106679257 sf0106678257 1 6679257 1.08E-52 1.92E-27
vg0105757117 sf0105756117 1 5757117 2.04E-33 9.42E-17
vg0106589855 sf0106588855 1 6589855 6.16E-27 2.89E-10
vg0317879120 sf0317877902 3 17879120 8.42E-26 1.25E-10
vg0112795014 sf0112793988 1 12795014 1.98E-21 8.61E-07
vg0229675574 sf0229669705 2 29675574 2.25E-16 NA
vg1223091766 sf1223058226 12 23091766 1.19E-15 NA
vg0105869431 sf0105868431 1 5869431 1.42E-13 8.41E-07
vg0105889711 sf0105888711 1 5889711 1.20E-11 9.39E-08
vg0105205583 sf0105204583 1 5205583 9.16E-11 3.12E-07
vg1223048348 sf1223014808 12 23048348 4.24E-09 2.75E-06
vg0105587028 sf0105586028 1 5587028 NA 2.87E-10
vg0106684533 sf0106683533 1 6684533 NA 2.46E-06