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 mr1371 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
vg0106301158 sf0106300158 1 6301158 5.01E-08 5.01E-08
vg0906975807 sf0906974807 9 6975807 1.63E-07 1.63E-07
vg0232486002 sf0232480133 2 32486002 1.72E-07 1.72E-07
vg0819431872 sf0819429159 8 19431872 4.22E-07 4.22E-07
vg0219786354 sf0219780486 2 19786354 9.53E-07 9.53E-07
vg0220283766 sf0220277898 2 20283766 1.94E-06 1.94E-06
vg1010572055 sf1010500876 10 10572055 2.94E-06 2.94E-06
vg0607824902 sf0607823903 6 7824902 3.58E-06 3.58E-06
vg0403579142 sf0403574744 4 3579142 4.29E-06 4.29E-06
vg0709078878 sf0709077884 7 9078878 4.35E-06 4.35E-06
vg0713837307 sf0713836314 7 13837307 4.87E-06 4.87E-06