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 mr1718 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
vg0321306372 sf0321304882 3 21306372 2.22E-24 2.71E-13
vg0321495504 sf0321494014 3 21495504 1.16E-23 9.33E-14
vg0318176270 sf0318175052 3 18176270 8.88E-22 2.73E-10
vg0318987746 sf0318986506 3 18987746 1.51E-20 5.98E-12
vg0319868224 sf0319866735 3 19868224 1.63E-16 1.51E-09
vg0320461954 sf0320460465 3 20461954 1.07E-15 1.73E-08
vg0318809268 sf0318808028 3 18809268 6.94E-15 1.75E-09
vg0318042622 sf0318041404 3 18042622 4.02E-14 4.64E-09
vg0318003091 sf0318001873 3 18003091 1.39E-13 7.87E-07
vg1215015294 sf1215012636 12 15015294 5.83E-13 NA
vg0529123966 sf0529061321 5 29123966 7.50E-13 NA
vg1217057350 sf1217051305 12 17057350 4.12E-12 NA
vg0318165198 sf0318163980 3 18165198 5.64E-12 1.45E-06
vg1207884606 sf1207882012 12 7884606 6.78E-11 1.67E-07
vg1217103792 sf1217097747 12 17103792 9.66E-11 3.03E-06
vg0319680247 sf0319678758 3 19680247 3.38E-10 7.79E-07
vg0321868776 sf0321867286 3 21868776 4.69E-10 2.03E-08
vg1204296378 sf1204295366 12 4296378 NA 6.65E-08
vg0320220294 sf0320218805 3 20220294 NA 3.53E-07
vg1204294767 sf1204293755 12 4294767 NA 4.95E-07
vg1214995135 sf1214992477 12 14995135 NA 8.52E-07
vg1214761316 sf1214758657 12 14761316 NA 1.51E-06
vg0100188252 sf0100187252 1 188252 NA 2.10E-06
vg0500016244 sf0500016244 5 16244 NA 4.94E-06