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 mr1576 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
vg1117614573 sf1117148429 11 17614573 1.25E-06 1.25E-06
vg0826164630 sf0826161916 8 26164630 1.35E-06 1.35E-06
vg1122447036 sf1121980907 11 22447036 3.96E-06 3.96E-06
vg1218127576 sf1218099012 12 18127576 4.59E-06 4.59E-06
vg1122487318 sf1122021189 11 22487318 6.43E-06 6.43E-06