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 mr1260 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
vg1009216003 sf1009144824 10 9216003 2.85E-13 NA
vg0423891208 sf0423706066 4 23891208 1.16E-12 4.11E-07
vg0205737044 sf0205737044 2 5737044 3.90E-12 NA
vg0721357298 sf0721356305 7 21357298 4.89E-12 NA
vg1128809059 sf1128285838 11 28809059 6.51E-12 NA
vg0118684354 sf0118683308 1 18684354 9.89E-11 4.78E-07
vg0132262398 sf0132261354 1 32262398 1.70E-10 2.13E-06
vg1009181623 sf1009110444 10 9181623 2.21E-10 5.37E-07
vg0706405260 sf0706404265 7 6405260 NA 1.68E-06
vg0906483706 sf0906482706 9 6483706 NA 8.79E-06