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 mr1629 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
vg1022145483 sf1022073957 10 22145483 8.87E-11 2.76E-07
vg0603465711 sf0603464712 6 3465711 3.70E-10 NA
vg1213285645 sf1213282983 12 13285645 4.83E-10 NA
vg1022121081 sf1022049555 10 22121081 5.83E-10 2.07E-08
vg0920930440 sf0920929959 9 20930440 7.02E-10 NA
vg0922095856 sf0922095375 9 22095856 1.05E-09 8.72E-06
vg0922167953 sf0922167472 9 22167953 1.80E-08 5.97E-06
vg0431121130 sf0430936019 4 31121130 4.54E-07 NA
vg0611066801 sf0611065802 6 11066801 3.21E-06 NA
vg1112750303 sf1112286624 11 12750303 6.58E-06 4.16E-06