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 mr1666 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
vg0710335701 sf0710334707 7 10335701 7.60E-12 NA
vg0400215019 sf0400214019 4 215019 4.95E-11 NA
vg1127488964 sf1127017351 11 27488964 8.23E-11 NA
vg0523862750 sf0523800171 5 23862750 8.46E-11 NA
vg0123795673 sf0123794629 1 23795673 8.63E-11 NA
vg0708824764 sf0708823769 7 8824764 3.95E-10 4.23E-06
vg0609473231 sf0609472232 6 9473231 2.46E-09 NA
vg1119186787 sf1118720475 11 19186787 1.33E-08 NA
vg0706938581 sf0706937586 7 6938581 2.11E-08 4.57E-07
vg1119511373 sf1119045061 11 19511373 5.24E-08 9.17E-07
vg1016679332 sf1016608105 10 16679332 1.40E-07 2.32E-06
vg1119431678 sf1118965366 11 19431678 NA 2.54E-07
vg1119330229 sf1118863917 11 19330229 NA 7.08E-07
vg0218857747 sf0218851878 2 18857747 NA 3.08E-06
vg0206217169 sf0206217169 2 6217169 NA 3.98E-06
vg0631229654 sf0631228656 6 31229654 NA 4.76E-06