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 mr1081 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
vg0222745001 sf0222739132 2 22745001 1.62E-15 7.23E-13
vg0224127834 sf0224121965 2 24127834 1.12E-09 5.20E-08
vg0321809345 sf0321807855 3 21809345 2.65E-08 NA
vg0222925074 sf0222919205 2 22925074 2.94E-08 5.66E-06
vg0222634177 sf0222628308 2 22634177 5.26E-08 4.25E-06
vg0323033808 sf0323032296 3 23033808 6.26E-08 NA
vg0224117343 sf0224111474 2 24117343 2.99E-07 2.88E-06
vg1109865477 sf1109860054 11 9865477 2.56E-06 1.02E-06
vg0406854976 sf0406850421 4 6854976 3.04E-06 7.51E-07
vg0408346647 sf0408341921 4 8346647 6.99E-06 NA
vg0406863364 sf0406858809 4 6863364 NA 3.09E-06