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 mr1095 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
vg0222724011 sf0222718142 2 22724011 2.67E-32 1.91E-25
vg0222719604 sf0222713735 2 22719604 3.26E-32 1.66E-25
vg0222765370 sf0222759501 2 22765370 7.33E-10 7.04E-07
vg0222634177 sf0222628308 2 22634177 1.08E-09 6.07E-06
vg0223818027 sf0223812158 2 23818027 2.09E-08 NA
vg0219771190 sf0219765322 2 19771190 2.44E-08 NA
vg0913973334 sf0913972333 9 13973334 2.68E-08 2.28E-06
vg0120651116 sf0120650071 1 20651116 5.18E-08 1.46E-06
vg0122405293 sf0122404248 1 22405293 1.89E-07 NA
vg0913952823 sf0913951822 9 13952823 7.69E-07 NA
vg0222879623 sf0222873754 2 22879623 8.02E-07 4.11E-07
vg0222681985 sf0222676116 2 22681985 2.05E-06 4.77E-06
vg0335688200 sf0335681069 3 35688200 3.62E-06 3.88E-07