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 mr1314 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
vg0210522452 sf0210522450 2 10522452 1.33E-07 1.33E-07
vg0431472905 sf0431287803 4 31472905 8.65E-07 8.65E-07
vg1117103676 sf1116637528 11 17103676 2.41E-06 2.41E-06
vg0506202477 sf0506202416 5 6202477 4.12E-06 4.12E-06
vg1114601521 sf1114137839 11 14601521 4.68E-06 4.68E-06
vg1005616080 sf1005632618 10 5616080 4.83E-06 4.83E-06