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 6.00E-69 1.11E-36
vg0106677498 sf0106676498 1 6677498 1.16E-67 1.01E-37
vg0106686481 sf0106685481 1 6686481 1.09E-65 4.13E-37
vg0317879120 sf0317877902 3 17879120 4.04E-31 3.04E-12
vg0112795014 sf0112793988 1 12795014 6.11E-21 NA
vg0104031438 sf0104030438 1 4031438 2.07E-20 2.39E-07
vg0229460554 sf0229454685 2 29460554 1.48E-17 NA
vg0103833171 sf0103832171 1 3833171 3.39E-16 1.65E-07
vg0105661905 sf0105660905 1 5661905 3.60E-16 2.87E-09
vg0224663231 sf0224657362 2 24663231 1.51E-14 1.49E-06
vg0306562863 sf0306561863 3 6562863 4.03E-14 3.74E-06
vg0106295051 sf0106294051 1 6295051 4.60E-12 9.42E-07
vg0106463385 sf0106462385 1 6463385 1.25E-09 4.26E-11
vg0102713715 sf0102712715 1 2713715 4.14E-09 2.71E-07
vg0106687292 sf0106686292 1 6687292 NA 1.06E-10
vg0604059961 sf0604058962 6 4059961 NA 5.02E-07
vg0106626230 sf0106625230 1 6626230 NA 1.04E-06
vg0105335997 sf0105334997 1 5335997 NA 2.64E-06
vg1117358853 sf1116892705 11 17358853 NA 3.82E-06