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 mr1695 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
vg0922500124 sf0922499643 9 22500124 2.52E-66 NA
vg0917445593 sf0917444592 9 17445593 9.98E-66 NA
vg0112313831 sf0112312805 1 12313831 1.30E-65 NA
vg0820721654 sf0820718941 8 20721654 1.54E-65 NA
vg1013261659 sf1013190429 10 13261659 3.12E-65 NA
vg0820742977 sf0820740264 8 20742977 2.34E-60 NA
vg0610128100 sf0610127101 6 10128100 NA 1.42E-12
vg0610021497 sf0610020498 6 10021497 NA 1.81E-12
vg0609896125 sf0609895126 6 9896125 NA 5.44E-10
vg0610006819 sf0610005820 6 10006819 NA 2.23E-09
vg0620971322 sf0620970325 6 20971322 NA 6.92E-09
vg0618988041 sf0618987044 6 18988041 NA 1.21E-07
vg0611638625 sf0611637626 6 11638625 NA 1.28E-07
vg0610205177 sf0610204178 6 10205177 NA 1.31E-07
vg0610022114 sf0610021115 6 10022114 NA 2.62E-07
vg0610397337 sf0610396338 6 10397337 NA 3.87E-07
vg0610136119 sf0610135120 6 10136119 NA 6.20E-07
vg0610419183 sf0610418184 6 10419183 NA 6.28E-07
vg0610444749 sf0610443750 6 10444749 NA 6.59E-07
vg0612260128 sf0612259129 6 12260128 NA 8.15E-07
vg0609837969 sf0609836970 6 9837969 NA 1.06E-06
vg0609822557 sf0609821558 6 9822557 NA 1.25E-06
vg0803804778 sf0803803781 8 3804778 NA 1.48E-06
vg0610132375 sf0610131376 6 10132375 NA 1.61E-06
vg0620951869 sf0620950872 6 20951869 NA 1.70E-06
vg0610191856 sf0610190857 6 10191856 NA 1.99E-06
vg0609993621 sf0609992622 6 9993621 NA 2.73E-06
vg0610904919 sf0610903920 6 10904919 NA 3.81E-06
vg0804605906 sf0804604909 8 4605906 NA 4.20E-06
vg0817393582 sf0817390868 8 17393582 NA 4.60E-06