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 mr1368 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
vg1019652686 sf1019581188 10 19652686 8.19E-09 1.90E-06
vg1019674394 sf1019602895 10 19674394 1.26E-08 1.37E-06
vg0801870143 sf0801869146 8 1870143 1.39E-08 NA
vg0629855440 sf0629854442 6 29855440 4.25E-08 NA
vg0506243358 sf0506243297 5 6243358 9.14E-08 NA
vg0810032310 sf0810031314 8 10032310 1.69E-07 4.93E-06
vg0336159623 sf0336152549 3 36159623 9.16E-06 2.39E-06