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 mr1625 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 3.61E-10 NA
vg0420788121 sf0420616164 4 20788121 4.89E-10 NA
vg1015795522 sf1015724292 10 15795522 8.06E-10 NA
vg0916820321 sf0916819320 9 16820321 7.64E-09 NA
vg0518472015 sf0518411501 5 18472015 1.28E-08 NA
vg0200805186 sf0200805186 2 805186 2.22E-07 NA
vg0227106783 sf0227100914 2 27106783 2.48E-07 2.24E-07
vg0122149426 sf0122148381 1 22149426 3.63E-06 NA
vg0224973322 sf0224967453 2 24973322 4.51E-06 7.10E-06