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 mr1054 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
vg1215178307 sf1215175643 12 15178307 2.51E-07 2.51E-07
vg1104978881 sf1104974692 11 4978881 4.55E-07 4.55E-07
vg1104978992 sf1104974803 11 4978992 5.13E-07 5.13E-07
vg0431411704 sf0431226602 4 31411704 1.22E-06 1.22E-06
vg0820865298 sf0820862585 8 20865298 1.66E-06 1.66E-06
vg0431472905 sf0431287803 4 31472905 2.14E-06 2.14E-06
vg1105269119 sf1105264870 11 5269119 2.17E-06 2.17E-06
vg1109631523 sf1109626100 11 9631523 3.81E-06 3.81E-06
vg0130689494 sf0130688450 1 30689494 3.85E-06 3.85E-06