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 mr1527 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
vg0907800067 sf0907799067 9 7800067 4.99E-08 NA
vg0907315834 sf0907314834 9 7315834 6.56E-08 NA
vg1021946954 sf1021875430 10 21946954 7.14E-08 NA
vg0141727155 sf0141726112 1 41727155 8.64E-08 NA
vg0315822851 sf0315821498 3 15822851 2.23E-07 2.53E-06
vg1005470235 sf1005486772 10 5470235 9.83E-07 1.58E-06
vg0404379553 sf0404375157 4 4379553 2.39E-06 NA
vg0141601194 sf0141600151 1 41601194 3.77E-06 NA
vg1000629872 sf1000628848 10 629872 7.56E-06 4.64E-06
vg1123146450 sf1122680321 11 23146450 8.63E-06 4.55E-06