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 mr1097 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
vg0130670983 sf0130669939 1 30670983 1.18E-15 4.13E-11
vg0704803343 sf0704802344 7 4803343 7.95E-09 NA
vg1203606223 sf1203605222 12 3606223 1.53E-08 NA
vg0706400044 sf0706399049 7 6400044 3.90E-08 NA
vg0726854885 sf0726853891 7 26854885 6.29E-08 NA
vg0135235698 sf0135234655 1 35235698 2.25E-07 4.46E-06
vg0138239162 sf0138238119 1 38239162 2.22E-06 4.79E-06
vg0135459224 sf0135458181 1 35459224 3.52E-06 NA