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 mr1740 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
vg0728386754 sf0728385762 7 28386754 1.65E-08 NA
vg1121916188 sf1121450059 11 21916188 2.54E-08 NA
vg0914863853 sf0914862852 9 14863853 5.60E-08 NA
vg0420822802 sf0420650845 4 20822802 5.85E-08 NA
vg0414221572 sf0414212285 4 14221572 6.77E-08 NA
vg0812030091 sf0812029096 8 12030091 4.73E-06 NA
vg1107474967 sf1107470712 11 7474967 NA 2.06E-06