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 mr1127 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
vg0220281817 sf0220275949 2 20281817 1.79E-09 5.11E-08
vg1220378676 sf1220350118 12 20378676 2.60E-07 7.03E-07
vg1104251780 sf1104247682 11 4251780 3.24E-07 3.96E-07
vg0428807864 sf0428622714 4 28807864 4.05E-06 4.65E-06
vg1218127576 sf1218099012 12 18127576 NA 2.19E-06
vg0824813029 sf0824810315 8 24813029 NA 9.21E-06