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 mr1347 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
vg0804309312 sf0804308315 8 4309312 1.11E-09 1.11E-09
vg0804327472 sf0804326475 8 4327472 2.37E-09 2.37E-09
vg0109353965 sf0109352941 1 9353965 1.41E-06 1.41E-06
vg0311016054 sf0311014772 3 11016054 1.90E-06 1.90E-06
vg0412125261 sf0412115972 4 12125261 2.13E-06 2.13E-06
vg1217863038 sf1217834472 12 17863038 2.62E-06 2.62E-06
vg1216567539 sf1216564832 12 16567539 4.37E-06 4.38E-06
vg0433049261 sf0432864148 4 33049261 4.97E-06 4.97E-06