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 mr1875 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
vg0122441656 sf0122440611 1 22441656 9.07E-08 9.07E-08
vg0122403766 sf0122402721 1 22403766 1.07E-06 1.07E-06
vg0705658607 sf0705657608 7 5658607 2.33E-06 2.33E-06
vg0122431881 sf0122430836 1 22431881 2.60E-06 2.60E-06
vg0615088161 sf0615087162 6 15088161 2.80E-06 2.80E-06
vg0123534125 sf0123533081 1 23534125 3.81E-06 3.81E-06