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 mr1687 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
vg0805992743 sf0805991746 8 5992743 1.36E-11 1.90E-09
vg0335297514 sf0335290383 3 35297514 1.60E-09 2.28E-07
vg0430475778 sf0430290656 4 30475778 4.85E-09 6.67E-07
vg0528836237 sf0528773592 5 28836237 5.75E-09 8.71E-07
vg0801697883 sf0801696886 8 1697883 7.38E-09 1.09E-06
vg1118023722 sf1117557580 11 18023722 9.33E-09 8.62E-07
vg1020531763 sf1020460242 10 20531763 1.85E-08 2.22E-06
vg0606329912 sf0606328913 6 6329912 2.99E-08 2.80E-06
vg1221176473 sf1221143019 12 21176473 9.25E-08 3.80E-06
vg0112179197 sf0112178171 1 12179197 1.00E-07 2.83E-06
vg0232480149 sf0232474280 2 32480149 3.64E-07 2.35E-06
vg0102103204 sf0102102204 1 2103204 4.63E-07 6.02E-07
vg0420718113 sf0420546156 4 20718113 NA 3.50E-06