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 mr1251 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
vg0216763637 sf0216757767 2 16763637 2.11E-14 8.21E-08
vg0810459509 sf0810458513 8 10459509 5.77E-13 NA
vg0425552229 sf0425367089 4 25552229 2.33E-12 NA
vg1219345800 sf1219317270 12 19345800 4.13E-12 NA
vg1125139237 sf1124673077 11 25139237 5.96E-12 NA
vg0124625557 sf0124624513 1 24625557 6.98E-10 NA