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 mr1864 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
vg0419266577 sf0419094615 4 19266577 3.71E-23 2.11E-08
vg0419218841 sf0419046879 4 19218841 5.83E-23 7.81E-10
vg0919336834 sf0919336424 9 19336834 1.77E-21 NA
vg0726514650 sf0726513656 7 26514650 3.63E-21 NA
vg0726517323 sf0726516329 7 26517323 4.30E-21 NA
vg0801794080 sf0801793083 8 1794080 3.33E-20 NA
vg0724771358 sf0724770364 7 24771358 9.59E-20 NA
vg0226696579 sf0226690710 2 26696579 2.58E-18 3.77E-06
vg0713218164 sf0713217171 7 13218164 2.78E-17 NA
vg1221167547 sf1221134093 12 21167547 6.73E-16 1.24E-06
vg1207983341 sf1207980747 12 7983341 5.45E-14 1.07E-06
vg0219780702 sf0219774834 2 19780702 NA 7.68E-07
vg0617621070 sf0617620073 6 17621070 NA 2.51E-06
vg0405006331 sf0405001770 4 5006331 NA 2.96E-06
vg0220326688 sf0220320820 2 20326688 NA 3.36E-06