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 mr1102 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
vg1115484424 sf1115020737 11 15484424 5.45E-08 1.92E-06
vg1115487596 sf1115023909 11 15487596 9.47E-08 2.14E-06
vg0217842911 sf0217837042 2 17842911 8.38E-07 2.09E-06
vg0431619094 sf0431433989 4 31619094 6.01E-06 NA
vg0217093878 sf0217088008 2 17093878 NA 4.89E-07