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 mr1158 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
vg0700193001 sf0700192001 7 193001 3.86E-12 8.75E-09
vg0700013444 sf0700012444 7 13444 5.99E-11 5.51E-10
vg0700009625 sf0700008625 7 9625 5.07E-09 9.38E-07
vg1001528261 sf1001527238 10 1528261 9.13E-07 NA
vg0904682424 sf0904681424 9 4682424 NA 2.28E-07
vg0615550236 sf0615549238 6 15550236 NA 1.89E-06
vg0622958104 sf0622957107 6 22958104 NA 4.02E-06
vg1224785662 sf1224752116 12 24785662 NA 4.04E-06