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 mr1595 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
vg0805854855 sf0805853858 8 5854855 1.97E-08 1.97E-08
vg0224215100 sf0224209231 2 24215100 5.50E-07 5.50E-07
vg0220960867 sf0220954999 2 20960867 8.31E-07 8.31E-07
vg0315010554 sf0315009201 3 15010554 9.11E-07 9.11E-07
vg1222907108 sf1222873547 12 22907108 2.99E-06 2.99E-06
vg0720879562 sf0720878569 7 20879562 3.26E-06 3.26E-06