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 mr1036 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
vg0331249126 sf0331242011 3 31249126 5.54E-14 4.25E-08
vg0331249150 sf0331242035 3 31249150 1.94E-13 3.15E-08
vg0401160440 sf0401155990 4 1160440 1.03E-09 NA
vg0205266925 sf0205266922 2 5266925 1.40E-09 5.00E-06
vg0802472843 sf0802471846 8 2472843 4.89E-09 NA
vg0125783821 sf0125782777 1 25783821 6.47E-09 NA
vg0205285361 sf0205285359 2 5285361 6.83E-08 7.55E-06
vg0922359301 sf0922358820 9 22359301 1.81E-06 7.54E-06