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 mr1642 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
vg1006757388 sf1006773011 10 6757388 4.02E-10 1.51E-06
vg0908755951 sf0908754950 9 8755951 1.75E-09 3.14E-06
vg1114456299 sf1113992616 11 14456299 2.82E-09 3.24E-06
vg0601801709 sf0601800710 6 1801709 4.17E-09 3.70E-06
vg0205989836 sf0205989836 2 5989836 1.16E-08 NA