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 mr1899 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
vg0414207961 sf0414198677 4 14207961 3.08E-08 3.09E-08
vg0407995614 sf0407990883 4 7995614 2.52E-07 2.52E-07
vg0401816201 sf0401811796 4 1816201 4.97E-07 4.96E-07
vg0101328541 sf0101327541 1 1328541 8.57E-07 8.55E-07
vg0407781751 sf0407777019 4 7781751 1.61E-06 1.62E-06
vg0716242048 sf0716241055 7 16242048 2.30E-06 2.30E-06
vg0724771358 sf0724770364 7 24771358 3.03E-06 3.02E-06
vg0721444375 sf0721443382 7 21444375 3.83E-06 3.83E-06
vg1126346911 sf1125875324 11 26346911 4.91E-06 4.91E-06
vg0721447322 sf0721446329 7 21447322 5.71E-06 5.63E-06
vg1003305785 sf1003304762 10 3305785 9.72E-06 9.69E-06