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 mr1002 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
vg1210055718 sf1210053129 12 10055718 1.67E-13 NA
vg1209814801 sf1209812211 12 9814801 3.08E-13 2.33E-06
vg1118152458 sf1117686316 11 18152458 8.30E-12 7.78E-06
vg0701811825 sf0701810826 7 1811825 2.07E-11 3.50E-07
vg1215036442 sf1215033784 12 15036442 3.37E-11 NA
vg0701855566 sf0701854567 7 1855566 3.91E-11 7.94E-07
vg0614347196 sf0614346197 6 14347196 1.72E-10 NA
vg1117717090 sf1117250946 11 17717090 1.83E-10 2.06E-06
vg1207623185 sf1207620587 12 7623185 6.09E-09 NA
vg0200459861 sf0200459861 2 459861 1.63E-08 NA
vg1212285604 sf1212282942 12 12285604 2.47E-07 3.45E-06
vg0235926582 sf0235920713 2 35926582 1.33E-06 NA
vg0207356509 sf0207356509 2 7356509 6.28E-06 NA