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 mr1945 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
vg1125118463 sf1124652303 11 25118463 6.10E-10 6.09E-10
vg1009189188 sf1009118009 10 9189188 5.24E-07 5.25E-07
vg0414121081 sf0414111796 4 14121081 8.27E-07 8.27E-07
vg1006139083 sf1006155619 10 6139083 8.56E-07 8.56E-07
vg0124119893 sf0124118849 1 24119893 9.03E-07 9.03E-07
vg1103603106 sf1103599009 11 3603106 1.47E-06 1.47E-06
vg1125162869 sf1124696709 11 25162869 1.57E-06 1.57E-06
vg0325923493 sf0325921511 3 25923493 1.73E-06 1.73E-06
vg0805790576 sf0805789579 8 5790576 2.08E-06 2.08E-06
vg1125082418 sf1124616258 11 25082418 2.61E-06 2.61E-06
vg1126292021 sf1125820434 11 26292021 4.49E-06 4.49E-06