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 mr1726 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
vg0711550113 sf0711549119 7 11550113 4.51E-20 NA
vg0619653506 sf0619652509 6 19653506 3.94E-19 NA
vg0232382098 sf0232376229 2 32382098 7.12E-19 NA
vg0701246321 sf0701245321 7 1246321 1.64E-18 NA
vg0604586643 sf0604585644 6 4586643 2.63E-18 NA
vg0620697439 sf0620696442 6 20697439 7.39E-18 NA
vg0820974361 sf0820971648 8 20974361 1.01E-15 1.57E-06
vg0914832451 sf0914831450 9 14832451 6.36E-15 3.99E-06
vg0404270383 sf0404265990 4 4270383 NA 2.73E-07
vg0400899653 sf0400898653 4 899653 NA 6.43E-07
vg0619779165 sf0619778168 6 19779165 NA 1.87E-06
vg0726108448 sf0726107454 7 26108448 NA 2.60E-06
vg0300939247 sf0300938245 3 939247 NA 3.62E-06