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 mr1742 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
vg1105905120 sf1105900872 11 5905120 4.77E-08 NA
vg0919811919 sf0919811438 9 19811919 9.15E-08 NA
vg0336030581 sf0336023450 3 36030581 6.13E-07 4.73E-07
vg0706563568 sf0706562573 7 6563568 8.38E-07 1.14E-06
vg0328867254 sf0328860307 3 28867254 3.18E-06 NA
vg0919898747 sf0919898266 9 19898747 4.29E-06 NA