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 mr1381 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
vg0101354617 sf0101353617 1 1354617 2.84E-07 2.84E-07
vg1221140689 sf1221107235 12 21140689 1.20E-06 1.20E-06
vg0415354509 sf0415345225 4 15354509 1.72E-06 1.72E-06
vg0401160396 sf0401155946 4 1160396 1.72E-06 1.72E-06
vg0316506661 sf0316505306 3 16506661 1.78E-06 1.78E-06
vg0515257168 sf0515199710 5 15257168 2.18E-06 2.18E-06
vg0127827967 sf0127826923 1 27827967 2.71E-06 2.71E-06
vg0714225909 sf0714224916 7 14225909 2.98E-06 2.98E-06
vg1206434711 sf1206433601 12 6434711 8.51E-06 8.43E-06