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 mr1519 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
vg0115180309 sf0115179283 1 15180309 1.39E-11 3.26E-07
vg0815709042 sf0815706328 8 15709042 6.05E-09 NA
vg0331565451 sf0331558328 3 31565451 1.35E-08 NA
vg1223431837 sf1223398297 12 23431837 5.68E-08 NA
vg0528836237 sf0528773592 5 28836237 6.00E-08 1.30E-06
vg0142527699 sf0142526655 1 42527699 5.93E-07 2.52E-06
vg1221698940 sf1221665487 12 21698940 9.41E-06 2.68E-06