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 mr1773 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
vg0623323376 sf0623322379 6 23323376 6.62E-08 4.57E-06
vg1022649587 sf1022578061 10 22649587 7.83E-08 5.90E-06
vg0105005584 sf0105004584 1 5005584 2.28E-07 3.55E-06
vg0613051683 sf0613050684 6 13051683 4.17E-06 NA
vg0706102792 sf0706101793 7 6102792 NA 2.12E-08