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 mr1601 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
vg0208607058 sf0208607057 2 8607058 9.89E-07 9.89E-07
vg1116240057 sf1115774927 11 16240057 1.70E-06 1.70E-06
vg0719105731 sf0719104738 7 19105731 1.76E-06 1.76E-06
vg0719042120 sf0719041127 7 19042120 1.89E-06 1.89E-06
vg1211224791 sf1211222127 12 11224791 2.05E-06 2.05E-06