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 mr1319 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
vg0138427451 sf0138426408 1 38427451 1.33E-10 NA
vg0134815001 sf0134813958 1 34815001 2.13E-09 NA
vg0432022826 sf0431837719 4 32022826 5.55E-09 NA
vg0104339492 sf0104338492 1 4339492 8.36E-09 NA
vg0131819741 sf0131818697 1 31819741 1.79E-08 NA
vg0430776773 sf0430591646 4 30776773 3.77E-07 NA
vg0719342498 sf0719341505 7 19342498 4.67E-07 NA
vg1013323230 sf1013251999 10 13323230 8.16E-06 4.99E-06
vg0704005849 sf0704004850 7 4005849 NA 1.67E-06
vg0208607058 sf0208607057 2 8607058 NA 6.02E-06
vg0411210363 sf0411201064 4 11210363 NA 6.77E-06