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 mr1729 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
vg0726931196 sf0726930202 7 26931196 3.89E-08 NA
vg1215178307 sf1215175643 12 15178307 5.20E-08 NA
vg0805580340 sf0805579343 8 5580340 6.52E-08 NA
vg1117492559 sf1117026414 11 17492559 9.59E-08 NA
vg0216594674 sf0216588804 2 16594674 1.12E-06 2.00E-06
vg0805469573 sf0805468576 8 5469573 1.59E-06 1.69E-07
vg0520620260 sf0520557701 5 20620260 4.64E-06 1.62E-06
vg0805562241 sf0805561244 8 5562241 4.71E-06 NA
vg1204385807 sf1204384795 12 4385807 NA 3.91E-06
vg0618125723 sf0618124726 6 18125723 NA 6.11E-06