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 mr1913 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
vg0222722732 sf0222716863 2 22722732 1.46E-20 8.68E-20
vg0224274396 sf0224268527 2 24274396 3.13E-09 NA
vg0223637309 sf0223631440 2 23637309 1.19E-08 3.25E-06
vg0224539399 sf0224533530 2 24539399 4.20E-06 5.66E-09
vg1007942238 sf1007957848 10 7942238 4.22E-06 3.03E-07
vg0222987671 sf0222981802 2 22987671 6.62E-06 5.47E-09
vg0315178643 sf0315177290 3 15178643 NA 5.65E-07
vg1112606104 sf1112142307 11 12606104 NA 3.90E-06
vg0406332555 sf0406327995 4 6332555 NA 4.55E-06