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 mr1015 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
vg0133229072 sf0133228028 1 33229072 7.44E-16 5.28E-10
vg0133450559 sf0133449515 1 33450559 6.80E-15 8.83E-12
vg0131768610 sf0131767566 1 31768610 6.98E-09 NA
vg1208143024 sf1208140430 12 8143024 2.79E-08 2.67E-06
vg0142706198 sf0142705154 1 42706198 6.23E-08 NA
vg0407370896 sf0407366165 4 7370896 6.98E-08 NA
vg0421062242 sf0420890297 4 21062242 1.72E-07 NA
vg0106917740 sf0106916740 1 6917740 7.43E-06 NA
vg1122346442 sf1121880313 11 22346442 NA 4.95E-06