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 mr1445 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
vg0431043984 sf0430858869 4 31043984 7.52E-07 9.57E-07
vg0712843936 sf0712842943 7 12843936 1.86E-06 1.11E-06
vg0420503850 sf0420331894 4 20503850 2.69E-06 3.25E-06
vg0626149778 sf0626148781 6 26149778 4.04E-06 3.02E-06
vg0221240541 sf0221234673 2 21240541 NA 1.80E-06
vg0214178491 sf0214172621 2 14178491 NA 2.12E-06
vg0127316647 sf0127315603 1 27316647 NA 2.96E-06
vg0214178528 sf0214172658 2 14178528 NA 3.04E-06
vg0319113443 sf0319112203 3 19113443 NA 3.63E-06
vg0616750117 sf0616749119 6 16750117 NA 3.76E-06