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 mr1242 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
vg0610557430 sf0610556431 6 10557430 9.66E-13 1.69E-06
vg0610584301 sf0610583302 6 10584301 1.37E-12 2.45E-07
vg0612270091 sf0612269092 6 12270091 9.58E-10 NA
vg0616527806 sf0616526808 6 16527806 2.06E-09 NA
vg1008794614 sf1008723476 10 8794614 9.54E-09 NA
vg1124122024 sf1123655894 11 24122024 9.88E-09 NA
vg0611779998 sf0611778999 6 11779998 1.85E-07 NA
vg0214439802 sf0214433932 2 14439802 9.43E-06 8.90E-07
vg0113506305 sf0113505279 1 13506305 NA 5.63E-07
vg0501793703 sf0501793686 5 1793703 NA 7.15E-07