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 mr1422 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
vg0610604799 sf0610603800 6 10604799 5.85E-17 4.02E-09
vg0610429989 sf0610428990 6 10429989 7.94E-17 4.43E-10
vg0617359224 sf0617358227 6 17359224 3.37E-11 NA
vg0725376226 sf0725375232 7 25376226 4.81E-11 NA
vg0705638810 sf0705637811 7 5638810 1.66E-10 NA
vg0612016261 sf0612015262 6 12016261 3.51E-10 NA
vg1215170290 sf1215167626 12 15170290 5.40E-10 4.51E-06
vg0610590324 sf0610589325 6 10590324 1.73E-09 8.03E-08
vg0611960936 sf0611959937 6 11960936 1.82E-09 4.01E-06
vg0616930764 sf0616929767 6 16930764 1.95E-09 2.66E-07
vg0610135843 sf0610134844 6 10135843 9.93E-09 2.87E-06
vg0717519774 sf0717518781 7 17519774 7.76E-08 4.14E-06
vg0610369827 sf0610368828 6 10369827 1.17E-07 6.35E-07
vg0918912379 sf0918911379 9 18912379 9.65E-07 5.11E-06
vg1219575210 sf1219546680 12 19575210 6.14E-06 NA