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 mr1759 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
vg0805963026 sf0805962029 8 5963026 3.98E-09 2.15E-07
vg0324965295 sf0324963375 3 24965295 1.46E-08 1.14E-07
vg0805900956 sf0805899959 8 5900956 1.98E-08 1.27E-07
vg0714140419 sf0714139426 7 14140419 1.11E-07 2.77E-06
vg0317372993 sf0317371803 3 17372993 7.59E-07 4.63E-06
vg0901298010 sf0901297010 9 1298010 1.89E-06 1.13E-06
vg0409221188 sf0409216461 4 9221188 3.59E-06 3.30E-06
vg1213717963 sf1213715301 12 13717963 NA 3.42E-06