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 mr1607 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
vg1224023966 sf1223990419 12 24023966 3.77E-08 NA
vg1215153462 sf1215150798 12 15153462 7.23E-08 NA
vg0722679489 sf0722678496 7 22679489 8.04E-08 NA
vg0515325210 sf0515267751 5 15325210 3.17E-07 NA
vg0330235697 sf0330228736 3 30235697 3.82E-07 1.94E-06
vg1124078197 sf1123612067 11 24078197 2.88E-06 1.95E-06
vg0103381628 sf0103380628 1 3381628 5.46E-06 3.30E-07
vg1204560575 sf1204559563 12 4560575 9.30E-06 2.55E-06
vg0315246434 sf0315245081 3 15246434 NA 3.48E-06
vg1116495021 sf1116029898 11 16495021 NA 3.96E-06
vg0820948192 sf0820945479 8 20948192 NA 4.33E-06