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 mr1573 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
vg1104978992 sf1104974803 11 4978992 9.99E-08 9.99E-08
vg0820888052 sf0820885339 8 20888052 1.89E-07 1.89E-07
vg0431411704 sf0431226602 4 31411704 2.00E-07 2.00E-07
vg0709984451 sf0709983457 7 9984451 4.02E-07 4.03E-07
vg1215178307 sf1215175643 12 15178307 1.02E-06 1.02E-06
vg0431614108 sf0431429003 4 31614108 1.51E-06 1.51E-06
vg0431472905 sf0431287803 4 31472905 1.90E-06 1.90E-06
vg1210206055 sf1210203466 12 10206055 2.08E-06 2.08E-06
vg1105269119 sf1105264870 11 5269119 2.33E-06 2.33E-06
vg1109631523 sf1109626100 11 9631523 4.81E-06 4.81E-06