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 mr1457 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
vg1218885208 sf1218856643 12 18885208 3.10E-08 NA
vg1011449672 sf1011378491 10 11449672 3.81E-08 8.55E-06
vg1011445819 sf1011374638 10 11445819 9.60E-08 6.72E-06
vg0419763927 sf0419591962 4 19763927 2.93E-07 5.42E-07
vg0402420137 sf0402415733 4 2420137 4.66E-06 8.31E-07
vg0402111251 sf0402106845 4 2111251 NA 2.77E-06