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 mr1700 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
vg0124426992 sf0124425948 1 24426992 4.59E-11 NA
vg0728941591 sf0728940599 7 28941591 5.29E-11 NA
vg0805049178 sf0805048181 8 5049178 1.27E-10 NA
vg1118365111 sf1117898969 11 18365111 1.92E-10 NA
vg0317137871 sf0317136685 3 17137871 2.00E-10 NA
vg0304933169 sf0304932171 3 4933169 1.21E-08 NA
vg0317132380 sf0317131194 3 17132380 1.29E-08 NA
vg0115887532 sf0115886506 1 15887532 1.33E-08 3.05E-06
vg0223427077 sf0223421208 2 23427077 2.67E-08 NA
vg0528836237 sf0528773592 5 28836237 NA 5.33E-07
vg0805992743 sf0805991746 8 5992743 NA 2.06E-06
vg0207665511 sf0207665511 2 7665511 NA 3.03E-06
vg0706162756 sf0706161757 7 6162756 NA 3.30E-06
vg0805950842 sf0805949845 8 5950842 NA 3.65E-06