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 mr1730 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
vg0413862399 sf0413853117 4 13862399 9.17E-11 9.17E-11
vg0413759612 sf0413750326 4 13759612 1.30E-09 1.30E-09
vg1110446917 sf1110441462 11 10446917 1.37E-07 1.37E-07
vg0416174940 sf0416002973 4 16174940 2.10E-06 2.10E-06
vg0618947595 sf0618946598 6 18947595 3.60E-06 3.60E-06
vg1009327905 sf1009256726 10 9327905 4.68E-06 4.68E-06