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 mr1648 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
vg0717125075 sf0717124082 7 17125075 3.47E-12 3.28E-07
vg0709448532 sf0709447538 7 9448532 2.83E-09 4.05E-08
vg0123708079 sf0123707035 1 23708079 1.30E-08 NA
vg0223522667 sf0223516798 2 23522667 3.62E-08 2.12E-06
vg0716573684 sf0716572691 7 16573684 3.70E-08 NA
vg0713442761 sf0713441768 7 13442761 4.90E-08 3.04E-07
vg0424181194 sf0423996055 4 24181194 6.91E-08 1.36E-06
vg0412479443 sf0412470158 4 12479443 9.88E-08 3.14E-07
vg0403204105 sf0403199708 4 3204105 2.58E-07 5.61E-07
vg0424121172 sf0423936033 4 24121172 2.31E-06 7.90E-06
vg0902278490 sf0902277490 9 2278490 3.09E-06 3.47E-06