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 mr1786 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
vg0620613402 sf0620612405 6 20613402 7.29E-09 9.87E-07
vg0223858890 sf0223853021 2 23858890 3.09E-08 3.40E-06
vg0315257196 sf0315255843 3 15257196 5.41E-08 NA
vg0208692453 sf0208692452 2 8692453 6.34E-08 1.75E-06
vg0816277211 sf0816274497 8 16277211 1.96E-07 2.25E-06
vg0113601714 sf0113600688 1 13601714 7.49E-06 NA
vg0825053682 sf0825050968 8 25053682 NA 4.51E-06