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 mr1175 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
vg0524581876 sf0524519297 5 24581876 2.52E-25 NA
vg1209240725 sf1209238134 12 9240725 4.37E-25 NA
vg0406791284 sf0406786729 4 6791284 1.37E-24 NA
vg0805623359 sf0805622362 8 5623359 1.48E-24 NA
vg0500701314 sf0500701314 5 701314 2.90E-24 NA
vg0203457728 sf0203457726 2 3457728 NA 1.44E-06
vg0131159971 sf0131158927 1 31159971 NA 6.96E-06