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 mr1728 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
vg0630343361 sf0630342363 6 30343361 3.47E-08 NA
vg1004886820 sf1004903357 10 4886820 4.23E-06 NA
vg0105772813 sf0105771813 1 5772813 NA 2.80E-06
vg0231885318 sf0231879449 2 31885318 NA 2.97E-06
vg0105957608 sf0105956608 1 5957608 NA 3.27E-06
vg0601639995 sf0601638996 6 1639995 NA 4.13E-06
vg1218508170 sf1218479606 12 18508170 NA 4.23E-06
vg0104617495 sf0104616495 1 4617495 NA 6.25E-06