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 mr1126 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
vg0619331736 sf0619330739 6 19331736 5.21E-12 NA
vg0621806974 sf0621805977 6 21806974 9.99E-12 NA
vg0722836934 sf0722835941 7 22836934 1.62E-11 NA
vg0523130102 sf0523067543 5 23130102 1.17E-10 NA
vg0206102860 sf0206102860 2 6102860 2.90E-10 NA
vg0520366263 sf0520303736 5 20366263 7.99E-10 2.36E-06
vg1009327905 sf1009256726 10 9327905 2.65E-08 7.82E-06
vg1122298599 sf1121832470 11 22298599 3.95E-07 4.89E-06
vg0318103151 sf0318101933 3 18103151 4.35E-07 1.72E-06