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 mr1284 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
vg0304141111 sf0304140113 3 4141111 3.31E-07 3.31E-07
vg0724952558 sf0724951564 7 24952558 3.31E-07 3.31E-07
vg1002920760 sf1002919737 10 2920760 9.97E-07 9.97E-07
vg1221649964 sf1221616511 12 21649964 1.10E-06 1.10E-06
vg0329626503 sf0329619543 3 29626503 4.80E-06 4.80E-06