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 mr1905 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
vg0907046341 sf0907045341 9 7046341 4.34E-07 4.34E-07
vg0216646059 sf0216640189 2 16646059 6.47E-07 6.47E-07
vg0505143979 sf0505143957 5 5143979 1.23E-06 1.23E-06
vg1019827961 sf1019756461 10 19827961 1.83E-06 1.83E-06
vg0506632181 sf0506632122 5 6632181 7.69E-06 7.69E-06