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 mr1414 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
vg0726426716 sf0726425722 7 26426716 1.10E-33 NA
vg0215206594 sf0215200724 2 15206594 1.01E-32 NA
vg0124311776 sf0124310732 1 24311776 1.25E-32 NA
vg0230671125 sf0230665256 2 30671125 2.80E-32 NA
vg1203908845 sf1203907844 12 3908845 2.95E-32 1.86E-06
vg0231620755 sf0231614886 2 31620755 5.47E-32 2.15E-06
vg1203908733 sf1203907732 12 3908733 5.80E-32 4.31E-07
vg0310767670 sf0310766586 3 10767670 4.61E-31 1.66E-06
vg0310729979 sf0310728895 3 10729979 5.72E-30 7.63E-06
vg0917631829 sf0917630828 9 17631829 NA 2.37E-08
vg0116413317 sf0116412291 1 16413317 NA 1.11E-06
vg0506633819 sf0506633760 5 6633819 NA 2.09E-06
vg0726459088 sf0726458094 7 26459088 NA 2.30E-06
vg1001183960 sf1001182937 10 1183960 NA 2.56E-06
vg0700622597 sf0700621597 7 622597 NA 2.97E-06
vg0713417596 sf0713416603 7 13417596 NA 3.72E-06
vg0430357265 sf0430172142 4 30357265 NA 4.15E-06