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 mr1057 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
vg0223029780 sf0223023911 2 23029780 2.31E-09 5.42E-08
vg1220271711 sf1220243153 12 20271711 4.22E-09 3.01E-06
vg1225586451 sf1225552846 12 25586451 4.23E-08 NA
vg1008388235 sf1008317097 10 8388235 5.23E-08 NA
vg0226136784 sf0226130915 2 26136784 9.29E-07 4.25E-06