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 mr1183 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
vg0910805763 sf0910804762 9 10805763 4.86E-14 NA
vg0813557256 sf0813554809 8 13557256 2.08E-11 NA
vg0306755101 sf0306754101 3 6755101 2.36E-11 NA
vg0432682186 sf0432497075 4 32682186 2.00E-10 NA
vg0300244541 sf0300243541 3 244541 2.79E-10 NA
vg0501172183 sf0501172167 5 1172183 1.54E-09 1.87E-06
vg0218455790 sf0218449921 2 18455790 5.88E-07 2.04E-06
vg0106102408 sf0106101408 1 6102408 6.31E-07 NA
vg0403035005 sf0403030609 4 3035005 1.98E-06 NA
vg0605381468 sf0605380469 6 5381468 2.43E-06 NA
vg0124173863 sf0124172819 1 24173863 NA 2.43E-06
vg0224292809 sf0224286940 2 24292809 NA 8.73E-06