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 mr1189 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
vg0724465712 sf0724464718 7 24465712 2.23E-21 NA
vg0229433488 sf0229427619 2 29433488 6.71E-21 NA
vg0918500604 sf0918499603 9 18500604 6.31E-20 NA
vg0127690868 sf0127689824 1 27690868 9.24E-20 NA
vg0400456619 sf0400455617 4 456619 3.37E-19 NA
vg1201655992 sf1201654992 12 1655992 1.38E-14 NA
vg0129717929 sf0129716884 1 29717929 NA 1.87E-06
vg0431921919 sf0431736814 4 31921919 NA 2.25E-06
vg0224387072 sf0224381203 2 24387072 NA 3.67E-06
vg1209080302 sf1209077711 12 9080302 NA 4.71E-06