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 mr1047 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
vg0229433488 sf0229427619 2 29433488 3.51E-13 NA
vg0724588571 sf0724587577 7 24588571 3.51E-13 NA
vg1015795522 sf1015724292 10 15795522 1.32E-12 NA
vg0420788121 sf0420616164 4 20788121 2.14E-12 NA
vg0916819608 sf0916818607 9 16819608 2.20E-12 NA
vg0920821502 sf0920821021 9 20821502 2.56E-10 NA
vg0410180309 sf0410171006 4 10180309 3.08E-10 2.52E-06
vg0224973322 sf0224967453 2 24973322 NA 3.43E-06
vg0819755231 sf0819752518 8 19755231 NA 4.04E-06
vg1003735001 sf1003733978 10 3735001 NA 5.71E-06