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 mr1612 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
vg0524606543 sf0524543963 5 24606543 4.34E-24 3.18E-14
vg0110400456 sf0110399432 1 10400456 5.96E-20 3.99E-09
vg0110450390 sf0110449366 1 10450390 1.27E-19 3.03E-09
vg0518201525 sf0518141011 5 18201525 1.97E-17 4.06E-06
vg0827030971 sf0827028257 8 27030971 2.99E-17 2.21E-06
vg0505969296 sf0505969235 5 5969296 1.10E-16 2.13E-06
vg0505957652 sf0505957591 5 5957652 1.35E-16 2.03E-06
vg0702261563 sf0702260564 7 2261563 2.64E-16 1.40E-06
vg0520054493 sf0519991969 5 20054493 4.06E-16 1.43E-06
vg0620513547 sf0620512550 6 20513547 8.42E-16 4.47E-06
vg0804253817 sf0804252820 8 4253817 9.55E-15 3.11E-06
vg0524480193 sf0524417614 5 24480193 NA 3.58E-09
vg0913973334 sf0913972333 9 13973334 NA 1.19E-06
vg0420837342 sf0420665385 4 20837342 NA 1.41E-06
vg0322179197 sf0322177704 3 22179197 NA 1.92E-06
vg0702566308 sf0702565309 7 2566308 NA 2.33E-06