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
vg1109729286 sf1109723863 11 9729286 1.45E-12 1.24E-09
vg1115484424 sf1115020737 11 15484424 2.54E-12 3.68E-08
vg1115480914 sf1115017227 11 15480914 7.17E-12 1.83E-09
vg1109779912 sf1109774489 11 9779912 3.29E-11 6.32E-08
vg1115482640 sf1115018953 11 15482640 3.36E-11 5.34E-11
vg1110437041 sf1110431586 11 10437041 1.23E-09 1.55E-08
vg0324994125 sf0324992205 3 24994125 7.12E-07 1.75E-06
vg0431427307 sf0431242205 4 31427307 3.37E-06 NA
vg0808441335 sf0808440339 8 8441335 3.44E-06 1.06E-06
vg0429002025 sf0428816883 4 29002025 4.01E-06 3.64E-06