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 mr1473 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
vg0228241702 sf0228235833 2 28241702 2.38E-08 2.39E-08
vg0230574938 sf0230569069 2 30574938 2.51E-08 2.51E-08
vg0230805438 sf0230799569 2 30805438 4.13E-08 4.14E-08
vg0626920669 sf0626919672 6 26920669 2.05E-07 2.06E-07
vg1001912776 sf1001911753 10 1912776 5.24E-07 5.25E-07
vg1001913135 sf1001912112 10 1913135 2.63E-06 2.64E-06
vg0121863168 sf0121862123 1 21863168 4.27E-06 4.28E-06
vg0234351024 sf0234345155 2 34351024 4.46E-06 4.47E-06
vg0801575988 sf0801574990 8 1575988 4.47E-06 4.48E-06