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 mr1168 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
vg0521573217 sf0521510658 5 21573217 7.46E-07 7.47E-07
vg0111350503 sf0111349479 1 11350503 1.68E-06 1.68E-06
vg0420546726 sf0420374770 4 20546726 1.94E-06 1.94E-06
vg1128769378 sf1128246157 11 28769378 2.46E-06 2.46E-06
vg1127791639 sf1127320025 11 27791639 4.22E-06 4.22E-06
vg0233989679 sf0233983810 2 33989679 4.53E-06 4.54E-06
vg1127775608 sf1127303994 11 27775608 5.14E-06 5.14E-06