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 mr1722 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
vg0335630368 sf0335623237 3 35630368 2.04E-13 7.44E-06
vg0113615260 sf0113614234 1 13615260 1.80E-12 NA
vg0414937528 sf0414928242 4 14937528 2.08E-12 NA
vg0230170128 sf0230164259 2 30170128 4.29E-12 2.13E-06
vg0902526765 sf0902525765 9 2526765 4.71E-12 NA
vg0233733433 sf0233727564 2 33733433 6.09E-12 7.60E-06
vg0408057094 sf0408052366 4 8057094 3.31E-11 4.88E-06
vg0224973322 sf0224967453 2 24973322 1.13E-10 NA
vg1218022526 sf1217993962 12 18022526 NA 1.62E-06