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 mr1028 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
vg0710323977 sf0710322983 7 10323977 8.33E-10 NA
vg0712999468 sf0712998475 7 12999468 2.12E-09 NA
vg1209158266 sf1209155675 12 9158266 5.19E-09 NA
vg0139101409 sf0139100366 1 39101409 1.09E-08 NA
vg0123863533 sf0123862489 1 23863533 1.30E-08 NA
vg0710554467 sf0710553473 7 10554467 7.28E-08 NA