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 mr1995 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
vg0101490991 sf0101489991 1 1490991 1.73E-18 NA
vg0405710877 sf0405706316 4 5710877 1.37E-16 NA
vg0104668106 sf0104667106 1 4668106 1.22E-15 NA
vg0224550253 sf0224544384 2 24550253 4.56E-15 NA
vg0402158888 sf0402154483 4 2158888 4.70E-14 NA
vg0223818027 sf0223812158 2 23818027 1.49E-11 NA
vg0818043217 sf0818040504 8 18043217 3.06E-10 2.84E-06
vg0715381494 sf0715380501 7 15381494 6.61E-10 3.99E-06
vg1017098914 sf1017027686 10 17098914 NA 3.31E-06
vg0921766254 sf0921765773 9 21766254 NA 4.79E-06