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 mr1326 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
vg1217549799 sf1217543754 12 17549799 1.95E-08 1.35E-07
vg0818736737 sf0818734024 8 18736737 8.99E-08 NA
vg1225407241 sf1225373637 12 25407241 5.24E-06 NA
vg1003735001 sf1003733978 10 3735001 8.17E-06 NA
vg1208174078 sf1208171484 12 8174078 NA 1.65E-06
vg1218168882 sf1218140318 12 18168882 NA 2.00E-06
vg0122689969 sf0122688924 1 22689969 NA 2.92E-06