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 mr1581 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
vg0114354546 sf0114353520 1 14354546 5.51E-15 NA
vg0719626509 sf0719625516 7 19626509 6.14E-14 NA
vg0817380259 sf0817377545 8 17380259 1.68E-13 NA
vg0316108526 sf0316107173 3 16108526 4.16E-13 NA
vg0616870219 sf0616869222 6 16870219 5.20E-13 NA
vg1208195076 sf1208192482 12 8195076 6.20E-11 NA
vg0319386807 sf0319385318 3 19386807 4.98E-10 1.10E-06
vg1109604230 sf1109598807 11 9604230 NA 3.67E-06
vg0320725270 sf0320723780 3 20725270 NA 4.70E-06