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 mr1979 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
vg1124179089 sf1123712959 11 24179089 2.57E-07 2.58E-07
vg0223525077 sf0223519208 2 23525077 4.90E-07 4.90E-07
vg0232481318 sf0232475449 2 32481318 9.21E-07 9.18E-07
vg1118023722 sf1117557580 11 18023722 2.39E-06 2.40E-06
vg0142427760 sf0142426716 1 42427760 3.47E-06 3.48E-06
vg0811404383 sf0811403388 8 11404383 3.73E-06 3.74E-06
vg1127563288 sf1127091675 11 27563288 4.86E-06 4.84E-06