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 mr1788 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
vg0906682620 sf0906681620 9 6682620 2.31E-11 4.74E-07
vg0429156078 sf0428970940 4 29156078 2.61E-11 5.55E-06
vg1217198502 sf1217192457 12 17198502 1.21E-08 NA
vg0419912063 sf0419740099 4 19912063 3.09E-08 NA
vg0710154939 sf0710153945 7 10154939 4.74E-08 NA
vg1017940885 sf1017869657 10 17940885 3.59E-07 5.34E-06
vg0206119753 sf0206119753 2 6119753 7.14E-06 4.19E-07