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 mr1727 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
vg0105725060 sf0105724060 1 5725060 8.74E-10 7.26E-06
vg0420200137 sf0420028179 4 20200137 2.79E-09 NA
vg0517975909 sf0517915395 5 17975909 5.08E-09 NA
vg1218165628 sf1218137064 12 18165628 5.53E-09 NA
vg0909065986 sf0909064985 9 9065986 6.77E-09 NA
vg0819439794 sf0819437081 8 19439794 1.25E-08 1.01E-06
vg0805950842 sf0805949845 8 5950842 2.00E-08 2.40E-07
vg0314727656 sf0314726343 3 14727656 3.49E-08 4.52E-06
vg0115887532 sf0115886506 1 15887532 3.53E-08 4.64E-06
vg0528836237 sf0528773592 5 28836237 NA 5.89E-07
vg1118023722 sf1117557580 11 18023722 NA 4.31E-06
vg0207699992 sf0207699991 2 7699992 NA 4.52E-06