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 mr1814 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
vg0819439794 sf0819437081 8 19439794 9.78E-09 NA
vg1127113140 sf1126641527 11 27113140 2.57E-08 NA
vg1013275525 sf1013204295 10 13275525 3.29E-08 1.12E-06
vg0603318281 sf0603317282 6 3318281 4.42E-08 NA
vg1217711180 sf1217705135 12 17711180 5.82E-08 NA
vg0434768134 sf0434583025 4 34768134 1.22E-07 3.94E-07
vg0232481318 sf0232475449 2 32481318 2.27E-07 3.55E-07
vg1125669886 sf1125203725 11 25669886 2.85E-07 4.01E-06